# HG changeset patch
# User galaxyp
# Date 1669921587 0
# Node ID aa86583676084d09198cede91f140aeddc77e786
# Parent  aa43ad3b2da693a0f0482477e409c909b728a823
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

diff -r aa43ad3b2da6 -r aa8658367608 404-urls.patch
--- a/404-urls.patch	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-diff -ruN FeatureFinderSuperHirn.xml FeatureFinderSuperHirn.xml
---- FeatureFinderSuperHirn.xml	2020-10-02 12:06:56.398572301 +0200
-+++ FeatureFinderSuperHirn.xml	2020-10-02 12:07:31.511153834 +0200
-@@ -105,6 +105,6 @@
-   <help><![CDATA[Finds mass spectrometric features in mass spectra.
- 
- 
--For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderSuperHirn.html]]></help>
-+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.6.0/html/UTILS_FeatureFinderSuperHirn.html]]></help>
-   <expand macro="references"/>
- </tool>
diff -r aa43ad3b2da6 -r aa8658367608 FeatureLinkerUnlabeledQT.xml
--- a/FeatureLinkerUnlabeledQT.xml	Fri Nov 06 19:59:16 2020 +0000
+++ b/FeatureLinkerUnlabeledQT.xml	Thu Dec 01 19:06:27 2022 +0000
@@ -1,13 +1,11 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Map Alignment]-->
-<tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Groups corresponding features from multiple maps.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,8 +14,13 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir in_cond.in &&
+#if $in_cond.in_select == "no"
+mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
+${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+#end if
 mkdir out &&
 #if $design:
   mkdir design &&
@@ -31,7 +34,11 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+#if $in_cond.in_select == "no"
+${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
+#end if
 -out
 'out/output.${gxy2omsext("consensusxml")}'
 #if $design:
@@ -49,12 +56,26 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
-    <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
-    <param name="keep_subelements" argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
+    <conditional name="in_cond">
+      <param name="in_select" type="select" label="Run tool in batch mode for -in">
+        <option value="no">No: process all datasets jointly</option>
+        <option value="yes">Yes: process each dataset in an independent job</option>
+      </param>
+      <when value="no">
+        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="consensusxml,featurexml" multiple="false" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/>
+      </when>
+    </conditional>
+    <param argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
+    <param argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help=""/>
-      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" help=""/>
+      <param name="nr_partitions" argument="-algorithm:nr_partitions" type="integer" optional="true" min="1" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution)" help=""/>
+      <param name="min_nr_diffs_per_bin" argument="-algorithm:min_nr_diffs_per_bin" type="integer" optional="true" min="5" value="50" label="If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region" help="RT regions will be extended until that number is reached"/>
+      <param name="min_IDscore_forTolCalc" argument="-algorithm:min_IDscore_forTolCalc" type="float" optional="true" value="1.0" label="If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation" help="Check your current score type!"/>
+      <param name="noID_penalty" argument="-algorithm:noID_penalty" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="If IDs are used: For the normalized distances, how high should the penalty for missing IDs be" help="0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away)"/>
       <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/>
       <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/>
       <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false">
@@ -64,10 +85,10 @@
       </section>
       <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false">
         <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/>
-        <param name="unit" argument="-algorithm:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help="">
+        <param name="unit" argument="-algorithm:distance_MZ:unit" type="select" optional="true" label="Unit of the 'max_difference' paramete" help="">
           <option value="Da" selected="true">Da</option>
           <option value="ppm">ppm</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="unit"/>
         </param>
         <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
         <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/>
@@ -75,17 +96,17 @@
       <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false">
         <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
         <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/>
-        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" type="select" optional="true" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
           <option value="enabled">enabled</option>
           <option value="disabled" selected="true">disabled</option>
-          <expand macro="list_string_san"/>
+          <expand macro="list_string_san" name="log_transform"/>
         </param>
       </section>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -98,13 +119,268 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_FeatureLinkerUnlabeledQT"/>
-    <expand macro="manutest_FeatureLinkerUnlabeledQT"/>
+  <tests><!-- TOPP_FeatureLinkerUnlabeledQT_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
+      </conditional>
+      <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="keep_subelements" value="false"/>
+      <section name="algorithm">
+        <param name="use_identifications" value="false"/>
+        <param name="nr_partitions" value="100"/>
+        <param name="min_nr_diffs_per_bin" value="50"/>
+        <param name="min_IDscore_forTolCalc" value="1.0"/>
+        <param name="noID_penalty" value="0.0"/>
+        <param name="ignore_charge" value="false"/>
+        <param name="ignore_adduct" value="true"/>
+        <section name="distance_RT">
+          <param name="max_difference" value="100.0"/>
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_MZ">
+          <param name="max_difference" value="0.3"/>
+          <param name="unit" value="Da"/>
+          <param name="exponent" value="2.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_intensity">
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="0.0"/>
+          <param name="log_transform" value="disabled"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_FeatureLinkerUnlabeledQT_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
+      </conditional>
+      <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="keep_subelements" value="true"/>
+      <section name="algorithm">
+        <param name="use_identifications" value="false"/>
+        <param name="nr_partitions" value="100"/>
+        <param name="min_nr_diffs_per_bin" value="50"/>
+        <param name="min_IDscore_forTolCalc" value="1.0"/>
+        <param name="noID_penalty" value="0.0"/>
+        <param name="ignore_charge" value="false"/>
+        <param name="ignore_adduct" value="true"/>
+        <section name="distance_RT">
+          <param name="max_difference" value="100.0"/>
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_MZ">
+          <param name="max_difference" value="0.3"/>
+          <param name="unit" value="Da"/>
+          <param name="exponent" value="2.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_intensity">
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="0.0"/>
+          <param name="log_transform" value="disabled"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_FeatureLinkerUnlabeledQT_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
+      </conditional>
+      <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="keep_subelements" value="false"/>
+      <section name="algorithm">
+        <param name="use_identifications" value="false"/>
+        <param name="nr_partitions" value="99999"/>
+        <param name="min_nr_diffs_per_bin" value="50"/>
+        <param name="min_IDscore_forTolCalc" value="1.0"/>
+        <param name="noID_penalty" value="0.0"/>
+        <param name="ignore_charge" value="false"/>
+        <param name="ignore_adduct" value="true"/>
+        <section name="distance_RT">
+          <param name="max_difference" value="100.0"/>
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_MZ">
+          <param name="max_difference" value="0.3"/>
+          <param name="unit" value="Da"/>
+          <param name="exponent" value="2.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_intensity">
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="0.0"/>
+          <param name="log_transform" value="disabled"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_FeatureLinkerUnlabeledQT_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
+      </conditional>
+      <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="keep_subelements" value="false"/>
+      <section name="algorithm">
+        <param name="use_identifications" value="true"/>
+        <param name="nr_partitions" value="100"/>
+        <param name="min_nr_diffs_per_bin" value="50"/>
+        <param name="min_IDscore_forTolCalc" value="1.0"/>
+        <param name="noID_penalty" value="0.0"/>
+        <param name="ignore_charge" value="false"/>
+        <param name="ignore_adduct" value="true"/>
+        <section name="distance_RT">
+          <param name="max_difference" value="100.0"/>
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_MZ">
+          <param name="max_difference" value="0.3"/>
+          <param name="unit" value="Da"/>
+          <param name="exponent" value="2.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_intensity">
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="0.0"/>
+          <param name="log_transform" value="disabled"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_FeatureLinkerUnlabeledQT_5 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
+      </conditional>
+      <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="keep_subelements" value="false"/>
+      <section name="algorithm">
+        <param name="use_identifications" value="false"/>
+        <param name="nr_partitions" value="100"/>
+        <param name="min_nr_diffs_per_bin" value="50"/>
+        <param name="min_IDscore_forTolCalc" value="1.0"/>
+        <param name="noID_penalty" value="0.0"/>
+        <param name="ignore_charge" value="false"/>
+        <param name="ignore_adduct" value="true"/>
+        <section name="distance_RT">
+          <param name="max_difference" value="200.0"/>
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_MZ">
+          <param name="max_difference" value="0.3"/>
+          <param name="unit" value="Da"/>
+          <param name="exponent" value="2.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_intensity">
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="0.0"/>
+          <param name="log_transform" value="disabled"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_FeatureLinkerUnlabeledQT_6 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
+      </conditional>
+      <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <param name="keep_subelements" value="false"/>
+      <section name="algorithm">
+        <param name="use_identifications" value="true"/>
+        <param name="nr_partitions" value="100"/>
+        <param name="min_nr_diffs_per_bin" value="50"/>
+        <param name="min_IDscore_forTolCalc" value="1.0"/>
+        <param name="noID_penalty" value="0.0"/>
+        <param name="ignore_charge" value="false"/>
+        <param name="ignore_adduct" value="true"/>
+        <section name="distance_RT">
+          <param name="max_difference" value="200.0"/>
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_MZ">
+          <param name="max_difference" value="0.3"/>
+          <param name="unit" value="Da"/>
+          <param name="exponent" value="2.0"/>
+          <param name="weight" value="1.0"/>
+        </section>
+        <section name="distance_intensity">
+          <param name="exponent" value="1.0"/>
+          <param name="weight" value="0.0"/>
+          <param name="log_transform" value="disabled"/>
+        </section>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Groups corresponding features from multiple maps.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureLinkerUnlabeledQT.html]]></help>
   <expand macro="references"/>
 </tool>
diff -r aa43ad3b2da6 -r aa8658367608 OMSSAAdapter.patch
--- a/OMSSAAdapter.patch	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
---- OMSSAAdapter.xml	2020-06-16 15:51:40.315400730 +0200
-+++ /tmp/OMSSAAdapter.xml	2020-06-16 15:50:23.536086074 +0200
-@@ -22,6 +22,7 @@
- mkdir database &&
- ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
- 
-+makeblastdb -dbtype prot -in 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
- ## Main program call
- 
- set -o pipefail &&
diff -r aa43ad3b2da6 -r aa8658367608 PepNovoAdapter.patch
--- a/PepNovoAdapter.patch	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
---- PepNovoAdapter.xml	2020-05-12 15:55:24.712831518 +0200
-+++ /tmp/PepNovoAdapter.xml	2020-05-12 15:36:31.267276757 +0200
-@@ -42,8 +42,13 @@
-   </configfiles>
-   <inputs>
-     <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
--    <param name="model_directory" argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help="">
--      <expand macro="list_string_san"/>
-+    <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help="">
-+        <options from_data_table="pepnovo_models">
-+            <column name="name" index="0"/>
-+            <column name="value" index="2"/>
-+            <filter type="unique_value" name="unique_set" column="0"/>
-+            <validator type="no_options" message="No model directory available"/>
-+        </options>
-     </param>
-     <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/>
-     <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/>
-@@ -51,8 +56,14 @@
-     <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/>
-     <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/>
-     <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/>
--    <param name="model" argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help="">
--      <expand macro="list_string_san"/>
-+    <param name="model" argument="-model" type="select" label="Name of the model that should be used" help="">
-+        <options from_data_table="pepnovo_models">
-+            <column name="name" index="1"/>
-+            <column name="value" index="1"/>
-+            <filter type="param_value" ref="model_directory" column="2"/>
-+            <filter type="unique_value" column="1"/>
-+            <validator type="no_options" message="No model available"/>
-+        </options>
-     </param>
-     <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help="">
-       <option value="TRYPSIN" selected="true">TRYPSIN</option>
diff -r aa43ad3b2da6 -r aa8658367608 filetypes.txt
--- a/filetypes.txt	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,85 +0,0 @@
-# CTD type    # Galaxy type
-# the following lines need to be at the top in order to ensure 
-# correct translation Galaxy->CTD type for the ambiguous cases
-# (should only be relevant for the autogenerated tests [which 
-# do not set the ftype of the inputs])
-txt           txt
-tsv           tabular
-
-##analysisXML
-# XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters 
-bioml         xml
-consensusXML  consensusxml
-# TODO csv is problematic, since csv often actually means tsv .. but not always
-csv           csv
-##dat
-dta           dta
-dta2d         dta2d
-edta          edta
-fa            fasta
-fas           fasta
-fasta         fasta
-FASTA         fasta
-featureXML    featurexml
-featurexml    featurexml
-# fid
-html          html
-HTML          html
-idXML         idxml
-##ini         txt
-json          json
-kroenik	      kroenik
-mascotXML     mascotxml
-mgf           mgf
-mrm           mrm
-ms            sirius.ms
-ms2           ms2
-msp           msp
-mzData        mzdata
-mzid          mzid
-# important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444
-mzML          mzml
-mzml          mzml
-mzq           mzq
-mzTab         mztab
-mzXML         mzxml
-novor         txt
-obo           obo
-# I guess this is the idXML output of omssa
-omssaXML      idxml
-osw           osw
-OSW           osw
-params        txt
-paramXML      paramxml
-fasta         peff
-peplist       peplist
-# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 .. but still in the tests
-pep.xml       pepxml
-pepXML        pepxml
-png           png
-PNG           png
-protXML       protxml
-psms          psms
-# TODO implement or use
-# psq
-pqp           pqp
-qcML          qcml
-spec.xml      spec.xml
-splib         splib
-sqMass        sqmass
-tandem.xml    tandem
-trafoXML      trafoxml
-traML         traml
-TraML         traml
-tab           tabular
-## MOVED TO TOP txt           txt
-raw           thermo.raw
-## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419
-xls           tsv
-XML           xml
-xml           xml
-xquest.xml    xquest.xml
-xsd           xml
-
-# TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml
-# cachedMzML    xml
diff -r aa43ad3b2da6 -r aa8658367608 fill_ctd.py
--- a/fill_ctd.py	Fri Nov 06 19:59:16 2020 +0000
+++ b/fill_ctd.py	Thu Dec 01 19:06:27 2022 +0000
@@ -32,7 +32,7 @@
     for k, v in e.items():
         if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
             mergeDicts(d[k], e[k])
-        elif k not in d and not isinstance(e[k], collections.abc.Mapping):
+        elif k not in d:
             d[k] = e[k]
         else:
             sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
@@ -135,9 +135,10 @@
 # insert the hc_args into the args
 mergeDicts(args, hc_args)
 
-if "adv_opts_cond" in args:
-    args.update(args["adv_opts_cond"])
-    del args["adv_opts_cond"]
+# put the contents of the advanced options section into the main dict
+if "adv_opts" in args:
+    args.update(args["adv_opts"])
+    del args["adv_opts"]
 
 # IDMapper has in and spectra:in params, in is used in out as format_source",
 # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
diff -r aa43ad3b2da6 -r aa8658367608 fill_ctd_clargs.py
--- a/fill_ctd_clargs.py	Fri Nov 06 19:59:16 2020 +0000
+++ b/fill_ctd_clargs.py	Thu Dec 01 19:06:27 2022 +0000
@@ -1,40 +1,70 @@
 #!/usr/bin/env python3
+
+import operator
 from argparse import ArgumentParser
+from functools import reduce  # forward compatibility for Python 3
 from io import StringIO
 
 from CTDopts.CTDopts import (
+    _Null,
     CTDModel,
     ModelTypeError,
     Parameters
 )
 
+
+def getFromDict(dataDict, mapList):
+    return reduce(operator.getitem, mapList, dataDict)
+
+
+def setInDict(dataDict, mapList, value):
+    getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value
+
+
 if __name__ == "__main__":
     # note add_help=False since otherwise arguments starting with -h will
     # trigger an error (despite allow_abbreviate)
     parser = ArgumentParser(prog="fill_ctd_clargs",
                             description="fill command line arguments"
-                            "into a CTD file and write the CTD file to",
+                            "into a CTD file and write the CTD file to stdout",
                             add_help=False, allow_abbrev=False)
-    parser.add_argument("--ctd", dest="ctd", help="input ctd file",
-                        metavar='CTD', default=None, required=True)
+    parser.add_argument("--ini_file", dest="ini_file", help="input ini file",
+                        metavar='INI', default=None, required=True)
+    parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file"
+                        "if given then optional parameters from the ini file"
+                        "will be filled with the defaults from this CTD file",
+                        metavar='CTD', default=None, required=False)
     args, cliargs = parser.parse_known_args()
+
     # load CTDModel
-    model = None
+    ini_model = None
     try:
-        model = CTDModel(from_file=args.ctd)
+        ini_model = CTDModel(from_file=args.ini_file)
     except ModelTypeError:
         pass
     try:
-        model = Parameters(from_file=args.ctd)
+        ini_model = Parameters(from_file=args.ini_file)
     except ModelTypeError:
         pass
-    assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd)
+    assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file)
 
     # get a dictionary of the ctd arguments where the values of the parameters
     # given on the command line are overwritten
-    margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True)
+    ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True)
+
+    if args.ctd_file:
+        ctd_model = CTDModel(from_file=args.ctd_file)
+        ctd_values = ctd_model.get_defaults()
+        for param in ini_model.get_parameters():
+            if not param.required and (param.default is None or type(param.default) is _Null):
+                lineage = param.get_lineage(name_only=True)
+                try:
+                    default = getFromDict(ctd_values, lineage)
+                except KeyError:
+                    continue
+                setInDict(ini_values, lineage, default)
 
     # write the ctd with the values taken from the dictionary
     out = StringIO()
-    ctd_tree = model.write_ctd(out, margs)
+    ctd_tree = ini_model.write_ctd(out, ini_values)
     print(out.getvalue())
diff -r aa43ad3b2da6 -r aa8658367608 generate-foo.sh
--- a/generate-foo.sh	Fri Nov 06 19:59:16 2020 +0000
+++ b/generate-foo.sh	Thu Dec 01 19:06:27 2022 +0000
@@ -8,17 +8,15 @@
 
     # get the tests from the CMakeLists.txt
     # 1st remove some tests
-    # - OpenSwathMzMLFileCacher with -convert_back argumen https://github.com/OpenMS/OpenMS/issues/4399
+    # - OpenSwathMzMLFileCacher with -convert_back argument https://github.com/OpenMS/OpenMS/issues/4399
     # - IDRipper PATH gets empty causing problems. TODO But overall the option needs to be handled differentlt
     # - several tools with duplicated input (leads to conflict when linking)
-    # - TOFCalibration inputs we extension (also in prepare_test_data) https://github.com/OpenMS/OpenMS/pull/4525
     # - MaRaCluster with -consensus_out (parameter blacklister: https://github.com/OpenMS/OpenMS/issues/4456)
     # - FileMerger with mixed dta dta2d input (ftype can not be specified in the test, dta can not be sniffed)
     # - some input files are originally in a subdir (degenerated cases/), but not in test-data
-    # - SeedListGenerator: https://github.com/OpenMS/OpenMS/issues/4404
     # - OpenSwathAnalyzer 9/10: cachedMzML (not supported yet)
-    # - FeatureFinderIdentification name clash of two tests https://github.com/OpenMS/OpenMS/pull/5002
-    # - TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    # - SiriusAdapter_4 depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
+    # - SiriusAdapter_10 should work in >2.8 https://github.com/OpenMS/OpenMS/issues/5869
     CMAKE=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake  |
         sed 's@${DATA_DIR_SHARE}/@@g' |
         grep -v 'OpenSwathMzMLFileCacher .*-convert_back' |
@@ -26,19 +24,9 @@
         grep -v "MaRaClusterAdapter.*-consensus_out"|
         grep -v "FileMerger_1_input1.dta2d.*FileMerger_1_input2.dta " |
         sed 's@degenerate_cases/@@g' |
-        grep -v 'TOPP_SeedListGenerator_3"' | 
         egrep -v 'TOPP_OpenSwathAnalyzer_test_3"|TOPP_OpenSwathAnalyzer_test_4"' |
-	egrep -v '"TOPP_FeatureFinderIdentification_4"' | 
-	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/')
-
-
-#         grep -v 'FileFilter.*-spectra:select_polarity ""' |
-#         grep -v 'MassTraceExtractor_2.ini ' |
-#         grep -v "FileMerger_6_input2.mzML.*FileMerger_6_input2.mzML" |
-#         grep -v "IDMerger_1_input1.idXML.*IDMerger_1_input1.idXML" |
-#         grep -v "degenerated_empty.idXML.*degenerated_empty.idXML" |
-#         grep -v "FeatureLinkerUnlabeledKD_1_output.consensusXML.*FeatureLinkerUnlabeledKD_1_output.consensusXML" |
-#         grep -v "FeatureLinkerUnlabeledQT_1_output.consensusXML.*FeatureLinkerUnlabeledQT_1_output.consensusXML" |
+        sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
+        grep -v '"TOPP_SiriusAdapter_10"')
 
     # 1st part is a dirty hack to join lines containing a single function call, e.g.
     # addtest(....
@@ -50,6 +38,7 @@
         # >&2 echo $line
         test_id=$(echo "$line" | cut -d" " -f 1)
         tool_id=$(echo "$line" | cut -d" " -f 2)
+        # >&2 echo "test_id $test_id"
         if [[ $test_id =~ _out_?[0-9]? ]]; then
             >&2 echo "    skip $test_id $line"
             continue
@@ -67,7 +56,7 @@
         tes="  <test>\n"
         line=$(fix_tmp_files "$line")
         line=$(unique_files "$line")
-        # >&2 echo $line
+        # >&2 echo LINE $line
         #if there is an ini file then we use this to generate the test
         #otherwise the ctd file is used
         #other command line parameters are inserted later into this xml
@@ -77,19 +66,23 @@
         else
             ini="ctd/$tool_id.ctd"
         fi
+        # >&2 echo "========================================================"
+        # >&2 echo "USING ini $ini"
         cli=$(echo $line |cut -d" " -f3- | sed 's/-ini [^ ]\+//')
 
         ctdtmp=$(mktemp)
-        #echo python3 fill_ctd_clargs.py --ctd $ini $cli
         # using eval: otherwise for some reason quoted values are not used properly ('A B' -> ["'A", "B'"])
-        # >&2 echo "python3 fill_ctd_clargs.py --ctd $ini $cli"
-        eval "python3 fill_ctd_clargs.py --ctd $ini $cli" > "$ctdtmp"
-        # echo $ctdtmp
+        # >&2 echo "python3 fill_ctd_clargs.py --ini_file $ini $cli" 
+        eval "python3 fill_ctd_clargs.py --ini_file $ini $cli" > "$ctdtmp"
+        # >&2 echo $ctdtmp
         # >&2 cat $ctdtmp
         testtmp=$(mktemp)
-        python3 $CTDCONVERTER/convert.py galaxy -i $ctdtmp -o $testtmp -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib > /dev/null
+        # >&2 echo CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7"
+        CTDConverter galaxy -i $ctdtmp -o $testtmp -s aux/tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p aux/hardcoded_params.json --tool-version $VERSION --test-only --test-unsniffable csv tsv txt dta dta2d edta mrm splib --test-condition "compare=sim_size" "delta_frac=0.7" > /dev/null
+        echo "<!-- $test_id -->"
         cat $testtmp | grep -v '<output.*file=""' # | grep -v 'CHEMISTRY/'
-        rm $ctdtmp $testtmp
+
+        rm "$ctdtmp" "$testtmp"
 
         #> /dev/null
 
@@ -130,23 +123,23 @@
 #(e.g. for prepare_test_data, e.g. CLI expects csv but test file is txt)
 #this function replaces the tmp file by the expected file. 
 function fix_tmp_files {
-#    >&2 echo "FIX $line"
+    # >&2 echo "FIX $line"
     ret=""
     for a in $@; do
-        if [[ ! $a =~ .tmp$ ]]; then
+        # >&2 echo "    a "$a
+        if [[ ! $a =~ .tmp$ ]] && [[ ! $a =~ _tmp_ ]]; then
             ret="$ret $a"
             continue
         fi
-#        >&2 echo "    a "$a
-        g=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
-#        >&2 echo "    g "$g
-        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$g)
+        diff_line=$(cat $OPENMSGIT/src/tests/topp/CMakeLists.txt $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | grep '\${DIFF}.*'"$a")
+        # >&2 echo "    diff_line "$diff_line
+        in1=$(sed 's/.*-in1 \([^ ]\+\).*/\1/' <<<$diff_line)
         # >&2 echo "    in1 "$in1
         if [[  "$a" != "$in1" ]]; then
             ret="$ret $a"
             continue
         fi
-        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$g)
+        in2=$(sed 's/.*-in2 \([^ ]\+\).*/\1/' <<<$diff_line)
         in2=$(basename $in2 | sed 's/)$//')
         # >&2 echo "    in2 "$in2
         if [[ -f "test-data/$in2" ]]; then
@@ -176,11 +169,11 @@
         fi
         ln -f -s $in1 test-data/$in2
     done
-    for i in test-data/*.tmp
-    do
+    
+    find test-data/ -name "*.tmp" -print0 | 
+    while IFS= read -r -d '' i; do 
         if [ ! -e test-data/$(basename $i .tmp) ]; then
             ln -s $(basename $i) test-data/$(basename $i .tmp)
-            #ln -s $(basename $i) test-data/$(basename $i .tmp)
         else
             ln -fs $(basename $i) test-data/$(basename $i .tmp)
         fi
@@ -194,14 +187,14 @@
 #     id=$1
 # | egrep -i "$id\_.*[0-9]+(_prepare\"|_convert)?"
 
-# TODO SiriusAdapter https://github.com/OpenMS/OpenMS/pull/5010
+    # TODO SiriusAdapter depends on online service which may timeout .. so keep disabled https://github.com/OpenMS/OpenMS/pull/5010
     cat $OPENMSGIT/src/tests/topp/CMakeLists.txt  $OPENMSGIT/src/tests/topp/THIRDPARTY/third_party_tests.cmake | sed 's/#.*$//'| sed 's/^\s*//; s/\s*$//' | grep -v "^$"  | awk '{printf("%s@NEWLINE@", $0)}' | sed 's/)@NEWLINE@/)\n/g' | sed 's/@NEWLINE@/ /g' | 
         sed 's/degenerate_cases\///' | 
         egrep -v "WRITEINI|WRITECTD|INVALIDVALUE|DIFF" | 
         grep add_test | 
         egrep "TOPP|UTILS" |
         sed 's@${DATA_DIR_SHARE}/@@g;'|
-        sed 's@${TMP_RIP_PATH}@dummy2.tmp@g'|
+        sed 's@${TMP_RIP_PATH}@./@g'|
         sed 's@TOFCalibration_ref_masses @TOFCalibration_ref_masses.txt @g; s@TOFCalibration_const @TOFCalibration_const.csv @'| 
 	sed 's/\("TOPP_SiriusAdapter_4".*\)-sirius:database all\(.*\)/\1-sirius:database pubchem\2/' |
     while read line
diff -r aa43ad3b2da6 -r aa8658367608 generate.sh
--- a/generate.sh	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-#!/usr/bin/env bash
-
-VERSION=2.6
-FILETYPES="filetypes.txt"
-PROFILE="20.05"
-## FILETYPES_RE=$(grep -v "^#" $FILETYPES | grep -v "^$" | cut -f 1 -d" " | tr '\n' '|' | sed 's/|$//'| sed 's/|/\\|/g')
-
-export tmp=$(mktemp -d)
-export CTDCONVERTER="$tmp/CTDConverter"
-
-###############################################################################
-## reset old data
-###############################################################################
-# rm $(ls *xml |grep -v macros)
-# rm -rf ctd
-# mkdir -p ctd
-# echo "" > prepare_test_data.sh
-
-###############################################################################
-## generate tests
-## also creates 
-## - conda environment (for executing the binaries) and 
-## - the git clone of OpenMS (for generating the tests)
-## - ctd files
-###############################################################################
-bash ./test-data.sh ./macros_autotest.xml
-
-###############################################################################
-## get the 
-## - conda package (for easy access and listing of the OpenMS binaries), 
-###############################################################################
-# if [ ! -d $OPENMSPKG ]; then
-# 	mkdir $OPENMSPKG/
-# 	wget -P $OPENMSPKG/ "$CONDAPKG"
-# 	tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C OpenMS$VERSION-pkg/
-#   rm $OPENMSPKG/"$(basename $CONDAPKG)"
-# fi
-
-###############################################################################
-## Get python libaries for CTD -> Galaxy conversion
-## TODO fix to main repo OR conda packkage if PRs are merged 
-###############################################################################
-# if [ ! -d CTDopts ]; then
-# 	# git clone https://github.com/genericworkflownodes/CTDopts CTDopts
-# 	git clone -b topic/no-1-2x https://github.com/bernt-matthias/CTDopts CTDopts
-# fi
-if [ ! -d $CTDCONVERTER ]; then
-	#git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
-	git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
-fi
-# export PYTHONPATH=$(pwd)/CTDopts
-###############################################################################
-## conversion ctd->xml 
-###############################################################################
-
-find . -maxdepth 0 -name "[A-Z]*xml" -delete
-source $(dirname $(which conda))/../etc/profile.d/conda.sh
-conda activate $tmp/OpenMS$VERSION-env
-python $CTDCONVERTER/convert.py galaxy -i ctd/*ctd -o ./ -s tools_blacklist.txt -f "$FILETYPES" -m macros.xml -t tool.conf  -p hardcoded_params.json --test-macros macros_autotest.xml --test-macros-prefix autotest_  --test-macros macros_test.xml --test-macros-prefix manutest_ --tool-version $VERSION --tool-profile $PROFILE > convert.out 2> convert.err
-if [[ "$?" -ne "0" ]]; then >&2 echo 'CTD -> XML conversion failed'; >&2 echo -e "stderr:\n$(cat convert.err)"; fi
-conda deactivate
-
-patch PepNovoAdapter.xml < PepNovoAdapter.patch
-patch OMSSAAdapter.xml < OMSSAAdapter.patch
-
-# https://github.com/OpenMS/OpenMS/pull/4984
-sed -i -e 's@http://www.openms.de/documentation/@http://www.openms.de/doxygen/release/2.6.0/html/@' ./*xml
-# https://github.com/OpenMS/OpenMS/pull/4984#issuecomment-702641976
-patch -p0 <404-urls.patch
-
-# #-b version log debug test in_type executable pepnovo_executable param_model_directory rt_concat_trafo_out param_id_pool
-
-# for i in A-E F-H I-L M-N O-P Q-Z
-# do
-# 	planemo t [$i]*xml --galaxy_branch release_20.05 --galaxy_python_version 3.7 --test_output $i.html --test_output_json $i.json &
-# done
diff -r aa43ad3b2da6 -r aa8658367608 hardcoded_params.json
--- a/hardcoded_params.json	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,236 +0,0 @@
-{
-	"#": "blacklist parameters",
-
-	"version": [{"value": "@"}],
-	"debug": [{"value": "@"}],
-	"algorithm:debug": [{"value": "@"}],
-	"java_memory": [{"value": "@"}],
-	"java_permgen": [{"value": "@"}],
-	"#": "type of input is always determined from the file extension ",
-	"in_type": [{"value": "@"}],
-
-	"#": "tool specific blacklist parameters",
-
-	"convert_back": [{"value": "@", "tools": ["OpenSwathMzMLFileCacher"]}],
-	"NET_executable": [{
-			"value": "@", 
-			"tools": ["FileConverter"]
-	}],
-
-
-	"params_file": [{"value": "@", "tools": ["SpectraSTSearchAdapter"]}],
-
-	"#": "TODO not usable in 2.5 https://github.com/OpenMS/OpenMS/issues/4456, corresponding test currently disabled",
-    	"consensus_out": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
-	"#": "TODO would need treatment as prefix-output",
-	"output_directory": [{"value": "@", "tools": ["MaRaClusterAdapter"]}],
-
-	"#": "hardcode parameter values",
-
-	"comet_version": [{
-		"value":"2016.01 rev. 3"
-	}],
-	"comet_executable": [{
-		"value":"comet"
-	}],
-	"crux_executable": [{
-		"value": "crux"
-	}],
-	"fido_executable": [{
-		"value":"Fido"
-	}],
-	"fidocp_executable": [{
-		"value":"FidoChooseParameters"
-	}],
-	"maracluster_executable": [{
-		"value":"/home/berntm/projects/tools-galaxyp/tools/openms/OpenMS2.5.0-git/THIRDPARTY/Linux/64bit/MaRaCluster/maracluster"
-	}],
-	"mascot_directory": [{
-		"value":"TODO"
-	}],
-	"myrimatch_executable": [{
-		"value":"myrimatch"
-	}],
-	"omssa_executable": [{
-		"value":"$(dirname $(realpath $(which omssacl)))/omssacl"
-	}],
-	"ThermoRaw_executable": [{
-		"value": "ThermoRawFileParser.exe", 
-		"tools": ["FileConverter"]
-	}],
-	"pepnovo_executable": [{
-		"value":"pepnovo"
-	}],
-	"percolator_executable": [{
-		"value":"percolator"
-	}],
-	"xtandem_executable": [{
-		"value":"xtandem"
-	}],
-	"executable": [
-		{
-			"value":"$(dirname $(realpath $(which luciphor2)))/luciphor2.jar",
-			"tools": ["LuciphorAdapter"]
-		}, {
-			"value":"/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar",
-			"tools": ["MSFraggerAdapter"]
-		}, {
-			"value":"$(msgf_plus -get_jar_path)",
-			"tools": ["MSGFPlusAdapter"]
-		}, {
-			"value": "/home/berntm/Downloads/novor/lib/novor.jar",
-			"tools": ["NovorAdapter"]
-		}, {
-			"value":"$(which sirius)",
-			"tools": ["SiriusAdapter", "AssayGeneratorMetabo"]
-		}, {
-			"value":"spectrast",
-			"tools": ["SpectraSTSearchAdapter"]
-		}
-	],
-	"r_executable": [{
-		"value":"R"
-	}],
-	"rscript_executable": [{
-		"value":"Rscript"
-	}],
-	"java_executable": [{
-		"value":"java"
-	}],
-	"log": [{
-		"value":"log.txt"
-	}],
-	"tempDirectory": [{
-		"value":"$TMP_DIR"
-	}],
-	"temp_data_directory": [{
-		"value":"$TMP_DIR"
-	}],
-	"algorithm:Preprocessing:tmp_dir": [{
-		"value":"$TMP_DIR"
-	}],
-	"no_progress": [{
-		"value": true
-	}],
-	"#": "only used in LuciphorAdapter at the moment, inconsistency will be fixed",
-	"num_threads": [{
-		"value":"${GALAXY_SLOTS:-1}"
-	}],
-	"threads": [{
-		"value": "${GALAXY_SLOTS:-1}"
-	}],
-	"sirius:cores": [{
-		"value": "${GALAXY_SLOTS:-1}"
-	}],
-
-	"#": "hardcode the outer loop threads for OpenSwathWorkflow",
-	"outer_loop_threads": [{
-			"value": "1", 
-			"tools": ["OpenSwathWorkflow"]
-	}],
-	"separator": [{
-		"value": ",",
-		"tools": ["IDMassAccuracy"]
-	}],
-
-	"#": "don't alow to copy data internally to save computation time for reloading",
-	"copy_data": [{
-		"value": "false",
-		"tools": ["MapAlignerTreeGuided"]
-	}],
-
-	"#": "overwrite/add Galaxy xml attributes of some parameters (names need to start with param_)",
-
-	"#": "test is not a hardcoded value since we need to set it in the tool tests", 
-	"test": [{
-		"CTD:type": "text",
-		"XML:type": "hidden"
-	}],
-
-	"#": "overwrite CTD attributes of some parameters (some are not possible, e.g. type)",
-
-	"#": "for some tools the user needs to select the desired output type since detection by extension makes no sense for galaxy tools",
-	"out_type": [{
-	    "CTD:required": true,
-	    "CTD:advanced": false
-	}],
-
-	"#": "SeedListGenerator with consensusXML input needs a dynamic number of outputs that depends on the content of the input, so we remove this options at the moment because its hard or impossible to implement in Galaxy, https://github.com/OpenMS/OpenMS/issues/4404 .. see also in parameter",
-	"#": "FileInfo, MapStatistics, SequenceCoverageCalculator wo -out just writes to stdout. not wanted here",
-	"#": "MzMLSplitter output prefix https://github.com/OpenMS/OpenMS/issues/4404",
-	"#": "IDRipper: blacklist out (is doing the same as the output-prefix out-path)",
-	"out": [{
-		"CTD:is_list": false, 
-		"tools": ["SeedListGenerator"]
-	}, {
-	 	"CTD:required": true,
-		"tools": ["FileInfo", "MapStatistics", "SequenceCoverageCalculator"]
-	}, {
-		"CTD:type": "output-prefix", 
-		"CTD:required": true,
-		"CTD:restrictions": "mzml",
-		"tools": ["MzMLSplitter"]
-	}, {
-		"value": "@", 
-		"tools": ["IDRipper"]
-	}],
-
-	"#": "Try to remove xml data type whereever possible",
-	"#": "XTandem Adapter output is called .xml in OMS which is to unspecific -> use Galaxy's bioml",
-	"xml_out": [{
-		"CTD:restrictions": "bioml",
-		"tools": ["XTandemAdapter"]
-	}],
-	
-	"#": "IDFileConverter remove xml",
-	"#": "OpenSwathWorkflow make in single file input and all outputs non-optional",
-        "#": "XFDR does not need xml .. redundant with xquest.xml TODO check if list is up to date with each new release",
-	"#": "SeedListGenerator: remove consensusXML https://github.com/OpenMS/OpenMS/issues/4404 .. see also out parameter",
-	"in": [{
-		"CTD:restrictions": "pepXML,protXML,mascotXML,omssaXML,bioml,psms,tsv,idXML,mzid,xquest.xml",
-		"tools": ["IDFileConverter"]
-	}, {
-		"CTD:is_list": false, 
-		"tools": ["OpenSwathWorkflow"]
-	}, {
-		"CTD:restrictions": "idXML,mzid,xquest.xml",
-		"tools": ["XFDR"]
-	}, {
-		"CTD:restrictions": "mzML,idXML,featureXML",
-		"tools": ["SeedListGenerator"]
-	}],
-
-	"#": "IDMapper has in and spectra:in params, in is used in out as format_source",
-	"#": "which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493", 
-	"spectra:in": [{
-		"CTD:name": "_in", 
-		"tools": ["IDMapper"]
-	}],
-
-	"#": "hardcoding prefix parameters which are not yet available in OMS but in CTDOpts https://github.com/OpenMS/OpenMS/pull/4527",
-	"#": "output-prefix",
-	"out_path": [{
-		"CTD:type": "output-prefix", 
-		"CTD:required": true,
-		"CTD:restrictions": "idXML",
-		"tools": ["IDRipper"]
-	}],
-	"outputDirectory": [{
-		"CTD:type": "output-prefix", 
-		"CTD:advanced": false,
-		"CTD:required": true,
-		"CTD:restrictions": "mzml",
-		"tools": ["OpenSwathFileSplitter"]
-	}],
-
-	"#": "OpenSwathDIAPreScoring: https://github.com/OpenMS/OpenMS/pull/4443",
-        "#": "SpectraSTSearchAdapter does not need xml .. redundant with pep.xml TODO check if list is up to date with each new release",
-	"output_files": [{
-		"CTD:required": true,
-		"tools": ["OpenSwathDIAPreScoring"]
-	}, {
-		"CTD:restrictions": "txt,tsv,pep.xml,pepXML,html",
-		"tools": ["SpectraSTSearchAdapter"]
-	
-	}]
-}
diff -r aa43ad3b2da6 -r aa8658367608 macros.xml
--- a/macros.xml	Fri Nov 06 19:59:16 2020 +0000
+++ b/macros.xml	Thu Dec 01 19:06:27 2022 +0000
@@ -3,14 +3,15 @@
      You can edit this file to add your own macros, if you so desire, or you can
      add additional macro files using the m/macros parameter -->
 <macros>
-  <token name="@TOOL_VERSION@">2.6</token>
-  <token name="@GALAXY_VERSION@">0</token>
+  <token name="@TOOL_VERSION@">2.8</token>
+  <token name="@VERSION_SUFFIX@">0</token>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">openms</requirement>
       <requirement type="package" version="@TOOL_VERSION@">openms-thirdparty</requirement>
-      <!-- makeblastdb for OMSSAAdapter -->
-      <requirement type="package" version="2.9.0">blast</requirement>
+      <!-- omssa (which has been excluded from 3rdparty) and makeblastdb for OMSSAAdapter -->
+      <requirement type="package" version="2.1.9">omssa</requirement>
+      <requirement type="package" version="2.13.0">blast</requirement>
       <!--<requirement type="package" version="5.0.0">tpp</requirement>-->
       <!-- for realpath (used e.g. in LuciphorAdapter) -->
 	  <!--<requirement type="package" version="8.25">coreutils</requirement>-->
@@ -21,6 +22,7 @@
   <xml name="stdio">
     <stdio>
       <regex match="std::bad_alloc" level="fatal_oom" description="Could not allocate memory"/>
+      <regex match="OutOfMemoryError" level="fatal_oom" description="Could not allocate memory"/>
       <regex match="Could not allocate metaspace" level="fatal_oom" description="Java memory Exception"/>
       <regex match="Cannot create VM thread" level="fatal_oom" description="Java memory Exception"/>
       <regex match="qUncompress: could not allocate enough memory to uncompress data" level="fatal_oom" description="Java memory Exception"/>
@@ -32,23 +34,15 @@
     </citations>
   </xml>
   <xml name="adv_opts_macro">
-    <conditional name="adv_opts_cond">
-      <param name="adv_opts_selector" type="select" label="Advanced Options">
-        <option value="basic" selected="True">Hide Advanced Options</option>
-        <option value="advanced">Show Advanced Options</option>
-      </param>
-      <when value="basic"/>
-      <when value="advanced">
-        <yield/>
-      </when>
-    </conditional>
+    <section name="adv_opts" title="Advanced Options" expanded="false">
+      <yield/>
+    </section>
   </xml>
 
   <!-- sanitizers and validators -->
-  <xml name="list_string_val">
-    <validator type="regex" message="parameter must not start with $">^[^$]</validator>
-    
-    <validator type="regex" message="a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
+  <xml name="list_string_val" token_name="">
+    <validator type="regex" message="parameter @NAME@: must not start with $">^[^$]</validator>
+    <validator type="regex" message="parameter @NAME@: a space separated list of string is needed (strings that contain spaces can be quoted with &quot;)">^ *((?:\"[^\"]*\" +)|(?:[^ \"]+ +))*((?:\"[^\"]*\")|(?:[^ \"]+)) *$</validator>
   </xml>
   <xml name="list_string_san">
     <sanitizer>
@@ -64,8 +58,8 @@
       </valid>
     </sanitizer>
   </xml>
-  <xml name="list_float_valsan">
-    <validator type="regex" message="a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator>
+  <xml name="list_float_valsan" token_name="">
+    <validator type="regex" message="parameter @NAME@: a space separated list of float values is required">^ *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?( *[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* *$</validator>
     <yield/>
     <sanitizer>
       <valid initial="string.digits">
@@ -78,8 +72,8 @@
       </valid>
     </sanitizer>
   </xml>
-  <xml name="list_integer_valsan">
-    <validator type="regex" message="a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
+  <xml name="list_integer_valsan" token_name="">
+    <validator type="regex" message="parameter @NAME@: a space separated list of integer values is required">^ *[+-]?[0-9]+( *[+-]?[0-9]+)* *$</validator>
     <yield/>
     <sanitizer>
       <valid initial="string.digits">
@@ -119,11 +113,11 @@
   </token>
 
 <token name="@EXT_FOO@"><![CDATA[#def oms2gxyext(o)
-    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
+    #set m={'txt': 'txt', 'tsv': 'tabular', 'bioml': 'xml', 'consensusXML': 'consensusxml', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fa': 'fasta', 'fas': 'fasta', 'fasta': 'fasta', 'FASTA': 'fasta', 'featureXML': 'featurexml', 'featurexml': 'featurexml', 'html': 'html', 'HTML': 'html', 'idXML': 'idxml', 'json': 'json', 'kroenik': 'kroenik', 'mascotXML': 'mascotxml', 'mgf': 'mgf', 'mrm': 'mrm', 'ms': 'sirius.ms', 'ms2': 'ms2', 'msp': 'msp', 'mzData': 'mzdata', 'mzid': 'mzid', 'mzML': 'mzml', 'mzml': 'mzml', 'mzq': 'mzq', 'mzQC': 'mzqc', 'mzTab': 'mztab', 'mzXML': 'mzxml', 'novor': 'txt', 'obo': 'obo', 'oms': 'sqlite', 'omssaXML': 'idxml', 'osw': 'osw', 'OSW': 'osw', 'params': 'txt', 'paramXML': 'paramxml', 'peplist': 'peplist', 'pep.xml': 'pepxml', 'pepXML': 'pepxml', 'png': 'png', 'PNG': 'png', 'protXML': 'protxml', 'psms': 'psms', 'pqp': 'pqp', 'qcML': 'qcml', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqMass': 'sqmass', 'tandem.xml': 'tandem', 'trafoXML': 'trafoxml', 'traML': 'traml', 'TraML': 'traml', 'tab': 'tabular', 'raw': 'thermo.raw', 'xls': 'tsv', 'XML': 'xml', 'xml': 'xml', 'xquest.xml': 'xquest.xml', 'xsd': 'xml'}
     #return m[o]
 #end def
 #def gxy2omsext(g)
-    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
+    #set m={'txt': 'txt', 'tabular': 'tsv', 'xml': 'bioml', 'consensusxml': 'consensusXML', 'csv': 'csv', 'dta': 'dta', 'dta2d': 'dta2d', 'edta': 'edta', 'fasta': 'fa', 'featurexml': 'featureXML', 'html': 'html', 'idxml': 'idXML', 'json': 'json', 'kroenik': 'kroenik', 'mascotxml': 'mascotXML', 'mgf': 'mgf', 'mrm': 'mrm', 'sirius.ms': 'ms', 'ms2': 'ms2', 'msp': 'msp', 'mzdata': 'mzData', 'mzid': 'mzid', 'mzml': 'mzML', 'mzq': 'mzq', 'mzqc': 'mzQC', 'mztab': 'mzTab', 'mzxml': 'mzXML', 'obo': 'obo', 'sqlite': 'oms', 'osw': 'osw', 'paramxml': 'paramXML', 'peff': 'fasta', 'peplist': 'peplist', 'pepxml': 'pep.xml', 'png': 'png', 'protxml': 'protXML', 'psms': 'psms', 'pqp': 'pqp', 'qcml': 'qcML', 'spec.xml': 'spec.xml', 'splib': 'splib', 'sqmass': 'sqMass', 'tandem': 'tandem.xml', 'trafoxml': 'trafoXML', 'traml': 'traML', 'thermo.raw': 'raw', 'tsv': 'xls', 'xquest.xml': 'xquest.xml'}
     #return m[g]
 #end def
 ]]></token></macros>
diff -r aa43ad3b2da6 -r aa8658367608 macros_autotest.xml
--- a/macros_autotest.xml	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27205 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<macros>
-  <xml name="autotest_AccurateMassSearch">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
-      <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
-      <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
-      <section name="db">
-        <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>
-        <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/>
-      </section>
-      <section name="algorithm">
-        <param name="mass_error_value" value="5.0"/>
-        <param name="mass_error_unit" value="ppm"/>
-        <param name="ionization_mode" value="positive"/>
-        <param name="isotopic_similarity" value="false"/>
-        <param name="use_feature_adducts" value="false"/>
-        <param name="keep_unidentified_masses" value="false"/>
-        <section name="mzTab">
-          <param name="exportIsotopeIntensities" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
-      <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
-      <section name="db">
-        <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
-        <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
-      </section>
-      <section name="algorithm">
-        <param name="mass_error_value" value="5.0"/>
-        <param name="mass_error_unit" value="ppm"/>
-        <param name="ionization_mode" value="positive"/>
-        <param name="isotopic_similarity" value="false"/>
-        <param name="use_feature_adducts" value="false"/>
-        <param name="keep_unidentified_masses" value="false"/>
-        <section name="mzTab">
-          <param name="exportIsotopeIntensities" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
-      <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
-      <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
-      <section name="db">
-        <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
-        <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
-      </section>
-      <section name="algorithm">
-        <param name="mass_error_value" value="5.0"/>
-        <param name="mass_error_unit" value="ppm"/>
-        <param name="ionization_mode" value="positive"/>
-        <param name="isotopic_similarity" value="false"/>
-        <param name="use_feature_adducts" value="false"/>
-        <param name="keep_unidentified_masses" value="false"/>
-        <section name="mzTab">
-          <param name="exportIsotopeIntensities" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_AssayGeneratorMetabo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="consensus_spectrum"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="consensus_spectrum"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="none"/>
-      <param name="method" value="consensus_spectrum"/>
-      <param name="use_exact_mass" value="false"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="true"/>
-      <param name="min_transitions" value="1"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="5.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="true"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="0.0"/>
-        <param name="max_fragment_mz" value="2000.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="precursor_recalibration_window" value="0.1"/>
-        <param name="precursor_recalibration_window_unit" value="Da"/>
-        <param name="min_fragment_mz" value="100.0"/>
-        <param name="max_fragment_mz" value="900.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
-      <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
-      <param name="out_type" value="tsv"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_annotation" value="sirius"/>
-      <param name="method" value="highest_intensity"/>
-      <param name="use_exact_mass" value="true"/>
-      <param name="exclude_ms2_precursor" value="false"/>
-      <param name="precursor_mz_distance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <param name="use_known_unknowns" value="false"/>
-      <param name="min_transitions" value="2"/>
-      <param name="max_transitions" value="3"/>
-      <param name="cosine_similarity_threshold" value="0.98"/>
-      <param name="transition_threshold" value="3.0"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="deisotoping">
-        <param name="use_deisotoper" value="false"/>
-        <param name="fragment_tolerance" value="1.0"/>
-        <param name="fragment_unit" value="ppm"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="1"/>
-        <param name="min_isopeaks" value="2"/>
-        <param name="max_isopeaks" value="3"/>
-        <param name="keep_only_deisotoped" value="false"/>
-        <param name="annotate_charge" value="false"/>
-      </section>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="10.0"/>
-        <param name="precursor_mz_tolerance_unit" value="ppm"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="100"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_BaselineFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="BaselineFilter_input.mzML"/>
-      <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="struc_elem_length" value="1.5"/>
-      <param name="struc_elem_unit" value="Thomson"/>
-      <param name="method" value="tophat"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ClusterMassTracesByPrecursor">
-</xml>
-  <xml name="autotest_ClusterMassTraces">
-</xml>
-  <xml name="autotest_CometAdapter">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:5000"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="1000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="5"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="CometAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <output name="pin_out" file="CometAdapter_1_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_mass_tolerance" value="3.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.50025"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.25"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep any known"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value=""/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:5000"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="1000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="5"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CometAdapter_2_prepared.mzML"/>
-      <output name="out" file="CometAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="CometAdapter_2_in.fasta"/>
-      <output name="pin_out" file="CometAdapter_2_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_mass_tolerance" value="3.0"/>
-      <param name="precursor_error_units" value="Da"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.50025"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.25"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep any known"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value=""/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:5000"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="20000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="3"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CometAdapter_3.mzML"/>
-      <output name="out" file="CometAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="CometAdapter_3.fasta"/>
-      <output name="pin_out" file="CometAdapter_3_out2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.01"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.0"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="3"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep known search unknown"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
-      <param name="variable_modifications" value="Acetyl (Protein N-term),Carbamidomethyl (N-term)"/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,pin_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_A_ions" value="false"/>
-        <param name="use_B_ions" value="true"/>
-        <param name="use_C_ions" value="false"/>
-        <param name="use_X_ions" value="false"/>
-        <param name="use_Y_ions" value="true"/>
-        <param name="use_Z_ions" value="false"/>
-        <param name="use_NL_ions" value="false"/>
-        <param name="second_enzyme" value=""/>
-        <param name="digest_mass_range" value="600:1200"/>
-        <param name="max_precursor_charge" value="5"/>
-        <param name="spectrum_batch_size" value="20000"/>
-        <param name="mass_offsets" value="0.0"/>
-        <param name="minimum_peaks" value="10"/>
-        <param name="minimum_intensity" value="0.0"/>
-        <param name="remove_precursor_peak" value="no"/>
-        <param name="remove_precursor_tolerance" value="1.5"/>
-        <param name="clear_mz_range" value="0:0"/>
-        <param name="max_variable_mods_in_peptide" value="3"/>
-        <param name="require_variable_mod" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="examples/FRACTIONS/BSA1_F1.mzML"/>
-      <output name="out" file="CometAdapter_4_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="examples/TOPPAS/data/BSA_Identification/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error" value="off"/>
-      <param name="fragment_mass_tolerance" value="0.01"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="fragment_bin_offset" value="0.0"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="num_enzyme_termini" value="fully"/>
-      <param name="missed_cleavages" value="3"/>
-      <param name="min_peptide_length" value="5"/>
-      <param name="max_peptide_length" value="63"/>
-      <param name="num_hits" value="5"/>
-      <param name="precursor_charge" value="0:0"/>
-      <param name="override_charge" value="keep known search unknown"/>
-      <param name="ms_level" value="2"/>
-      <param name="activation_method" value="ALL"/>
-      <param name="max_fragment_charge" value="3"/>
-      <param name="clip_nterm_methionine" value="false"/>
-      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
-      <param name="variable_modifications" value="Met-loss (Protein N-term M)"/>
-      <param name="binary_modifications" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CompNovoCID">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CompNovoCID_1_input.mzML"/>
-      <output name="out" file="CompNovoCID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="algorithm">
-        <param name="max_number_aa_per_decomp" value="4"/>
-        <param name="tryptic_only" value="true"/>
-        <param name="precursor_mass_tolerance" value="0.3"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="max_number_pivot" value="9"/>
-        <param name="max_subscore_number" value="40"/>
-        <param name="decomp_weights_precision" value="0.01"/>
-        <param name="double_charged_iso_threshold" value="0.6"/>
-        <param name="max_mz" value="2000.0"/>
-        <param name="min_mz" value="200.0"/>
-        <param name="max_isotope_to_score" value="3"/>
-        <param name="max_decomp_weight" value="450.0"/>
-        <param name="max_isotope" value="3"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="estimate_precursor_mz" value="true"/>
-        <param name="number_of_prescoring_hits" value="250"/>
-        <param name="fixed_modifications" value=""/>
-        <param name="variable_modifications" value=""/>
-        <param name="residue_set" value="Natural19WithoutI"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CompNovo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="CompNovo_1_input.mzML"/>
-      <output name="out" file="CompNovo_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="algorithm">
-        <param name="max_number_aa_per_decomp" value="4"/>
-        <param name="tryptic_only" value="true"/>
-        <param name="precursor_mass_tolerance" value="0.3"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="max_number_pivot" value="9"/>
-        <param name="max_subscore_number" value="40"/>
-        <param name="decomp_weights_precision" value="0.01"/>
-        <param name="double_charged_iso_threshold" value="0.6"/>
-        <param name="max_mz" value="2000.0"/>
-        <param name="min_mz" value="200.0"/>
-        <param name="max_isotope_to_score" value="3"/>
-        <param name="max_decomp_weight" value="450.0"/>
-        <param name="max_isotope" value="3"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="estimate_precursor_mz" value="true"/>
-        <param name="number_of_prescoring_hits" value="250"/>
-        <param name="fixed_modifications" value=""/>
-        <param name="variable_modifications" value=""/>
-        <param name="residue_set" value="Natural19WithoutI"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ConsensusID">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="PEPMatrix"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="PAM30MS"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_2_input.featureXML"/>
-      <output name="out" file="ConsensusID_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="average"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_3_input.consensusXML"/>
-      <output name="out" file="ConsensusID_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="PEPMatrix"/>
-      <section name="filter">
-        <param name="considered_hits" value="6"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="PEPIons"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_1_input.idXML"/>
-      <output name="out" file="ConsensusID_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="false"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.5"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="false"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_6_input.idXML"/>
-      <output name="out" file="ConsensusID_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="true"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="true"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusID_8_input.idXML"/>
-      <output name="out" file="ConsensusID_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="rt_delta" value="0.1"/>
-      <param name="mz_delta" value="0.1"/>
-      <param name="per_spectrum" value="true"/>
-      <param name="algorithm" value="best"/>
-      <section name="filter">
-        <param name="considered_hits" value="0"/>
-        <param name="min_support" value="0.0"/>
-        <param name="count_empty" value="false"/>
-        <param name="keep_old_scores" value="true"/>
-      </section>
-      <section name="PEPIons">
-        <param name="mass_tolerance" value="0.5"/>
-        <param name="min_shared" value="2"/>
-      </section>
-      <section name="PEPMatrix">
-        <param name="matrix" value="identity"/>
-        <param name="penalty" value="5"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ConsensusMapNormalizer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="accession_filter" value=""/>
-        <param name="description_filter" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
-      <output name="out" file="ConsensusMapNormalizer_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="algorithm_type" value="robust_regression"/>
-      <param name="ratio_threshold" value="0.67"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CruxAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="custom_enzyme" value=""/>
-        <param name="decoy_prefix" value="decoy_"/>
-        <param name="deisotope" value="false"/>
-        <param name="report_decoys" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="extra_index_args" value=""/>
-      <param name="extra_search_args" value=""/>
-      <param name="extra_percolator_args" value=""/>
-      <param name="precursor_mass_tolerance" value="10.0"/>
-      <param name="precursor_mass_units" value="ppm"/>
-      <param name="fragment_bin_offset" value="0.0"/>
-      <param name="fragment_bin_width" value="0.02"/>
-      <param name="isotope_error" value=""/>
-      <param name="run_percolator" value="false"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="digestion" value="full-digest"/>
-      <param name="allowed_missed_cleavages" value="0"/>
-      <param name="decoy_format" value="peptide-reverse"/>
-      <param name="keep_terminal_aminos" value="NC"/>
-      <param name="cterm_modifications" value=""/>
-      <param name="nterm_modifications" value=""/>
-      <param name="modifications" value=""/>
-      <param name="test_fdr" value="0.01"/>
-      <param name="train_fdr" value="0.01"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_CVInspector">
-</xml>
-  <xml name="autotest_DatabaseFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_1.fasta"/>
-      <param name="id" value="DatabaseFilter_1.idXML"/>
-      <param name="method" value="whitelist"/>
-      <output name="out" file="DatabaseFilter_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_1.fasta"/>
-      <param name="id" value="DatabaseFilter_1.idXML"/>
-      <param name="method" value="blacklist"/>
-      <output name="out" file="DatabaseFilter_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_3.fasta"/>
-      <param name="id" value="DatabaseFilter_3.mzid"/>
-      <param name="method" value="whitelist"/>
-      <output name="out" file="DatabaseFilter_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DatabaseFilter_3.fasta"/>
-      <param name="id" value="DatabaseFilter_3.mzid"/>
-      <param name="method" value="blacklist"/>
-      <output name="out" file="DatabaseFilter_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_DatabaseSuitability">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
-      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
-      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
-      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="algorithm">
-        <param name="no_rerank" value="false"/>
-        <param name="reranking_cutoff_percentile" value="0.01"/>
-        <param name="FDR" value="0.8"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
-      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
-      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
-      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="algorithm">
-        <param name="no_rerank" value="false"/>
-        <param name="reranking_cutoff_percentile" value="0.9"/>
-        <param name="FDR" value="1.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
-      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
-      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
-      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="algorithm">
-        <param name="no_rerank" value="true"/>
-        <param name="reranking_cutoff_percentile" value="0.01"/>
-        <param name="FDR" value="0.9"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_Decharger">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Decharger_input.featureXML"/>
-      <output name="out_cm" file="Decharger_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_fm" file="Decharger_output_fm.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="outpairs" file="Decharger_p_output.tmp" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <section name="FeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="10"/>
-          <param name="charge_span_max" value="4"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.1"/>
-          <param name="potential_adducts" value="&quot;H:+:0.7&quot; &quot;Na:+:0.1&quot; &quot;(2)H4H-4:0:0.1:-2:heavy&quot;"/>
-          <param name="max_neutrals" value="0"/>
-          <param name="max_minority_bound" value="2"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG,outpairs_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_DecoyDatabase">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_1.fasta"/>
-      <output name="out" file="DecoyDatabase_1_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="true"/>
-      <param name="type" value="protein"/>
-      <param name="method" value="reverse"/>
-      <param name="enzyme" value="Trypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value=""/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="42"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_1.fasta"/>
-      <output name="out" file="DecoyDatabase_2_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="false"/>
-      <param name="type" value="protein"/>
-      <param name="method" value="shuffle"/>
-      <param name="enzyme" value="Trypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value="KRP"/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="42"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_1.fasta"/>
-      <output name="out" file="DecoyDatabase_3_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="false"/>
-      <param name="type" value="protein"/>
-      <param name="method" value="shuffle"/>
-      <param name="enzyme" value="Chymotrypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value="KR"/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="seed" value="42"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DecoyDatabase_4.fasta"/>
-      <output name="out" file="DecoyDatabase_4_out.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="decoy_string" value="blabla"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="only_decoy" value="false"/>
-      <param name="type" value="RNA"/>
-      <param name="method" value="reverse"/>
-      <param name="enzyme" value="Trypsin"/>
-      <section name="Decoy">
-        <param name="non_shuffle_pattern" value=""/>
-        <param name="keepPeptideNTerm" value="true"/>
-        <param name="keepPeptideCTerm" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_DeMeanderize">
-</xml>
-  <xml name="autotest_DigestorMotif">
-</xml>
-  <xml name="autotest_Digestor">
-</xml>
-  <xml name="autotest_DTAExtractor">
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DTAExtractor_1_input.mzML"/>
-      <param name="out" value="DTAExtractor"/>
-      <param name="mz" value=":"/>
-      <param name="rt" value=":61"/>
-      <param name="level" value="1,2,3"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DTAExtractor_1_input.mzML"/>
-      <param name="out" value="DTAExtractor"/>
-      <param name="mz" value=":"/>
-      <param name="rt" value=":"/>
-      <param name="level" value="1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="DTAExtractor_1_input.mzML"/>
-      <param name="out" value="DTAExtractor"/>
-      <param name="mz" value=":1000"/>
-      <param name="rt" value=":"/>
-      <param name="level" value="2"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_EICExtractor">
-</xml>
-  <xml name="autotest_Epifany">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="conservative_fdr" value="true"/>
-        <param name="min_psms_extreme_probability" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="Epifany_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idxml"/>
-      <param name="protein_fdr" value="false"/>
-      <param name="greedy_group_resolution" value="none"/>
-      <param name="max_psms_extreme_probability" value="1.0"/>
-      <section name="algorithm">
-        <param name="psm_probability_cutoff" value="0.001"/>
-        <param name="top_PSMs" value="1"/>
-        <param name="keep_best_PSM_only" value="true"/>
-        <param name="update_PSM_probabilities" value="true"/>
-        <param name="user_defined_priors" value="false"/>
-        <param name="annotate_group_probabilities" value="true"/>
-        <param name="use_ids_outside_features" value="false"/>
-        <section name="model_parameters">
-          <param name="prot_prior" value="0.7"/>
-          <param name="pep_emission" value="0.1"/>
-          <param name="pep_spurious_emission" value="0.001"/>
-          <param name="pep_prior" value="0.1"/>
-          <param name="regularize" value="false"/>
-          <param name="extended_model" value="false"/>
-        </section>
-        <section name="loopy_belief_propagation">
-          <param name="scheduling_type" value="priority"/>
-          <param name="convergence_threshold" value="1e-05"/>
-          <param name="dampening_lambda" value="0.001"/>
-          <param name="max_nr_iterations" value="2147483647"/>
-          <param name="p_norm_inference" value="1.0"/>
-        </section>
-        <section name="param_optimize">
-          <param name="aucweight" value="0.3"/>
-          <param name="conservative_fdr" value="true"/>
-          <param name="regularized_fdr" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="conservative_fdr" value="true"/>
-        <param name="min_psms_extreme_probability" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_2_input.consensusXML"/>
-      <output name="out" file="Epifany_2_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="protein_fdr" value="false"/>
-      <param name="greedy_group_resolution" value="none"/>
-      <param name="max_psms_extreme_probability" value="1.0"/>
-      <section name="algorithm">
-        <param name="psm_probability_cutoff" value="0.001"/>
-        <param name="top_PSMs" value="1"/>
-        <param name="keep_best_PSM_only" value="true"/>
-        <param name="update_PSM_probabilities" value="true"/>
-        <param name="user_defined_priors" value="false"/>
-        <param name="annotate_group_probabilities" value="true"/>
-        <param name="use_ids_outside_features" value="false"/>
-        <section name="model_parameters">
-          <param name="prot_prior" value="0.7"/>
-          <param name="pep_emission" value="0.1"/>
-          <param name="pep_spurious_emission" value="0.001"/>
-          <param name="pep_prior" value="0.1"/>
-          <param name="regularize" value="false"/>
-          <param name="extended_model" value="false"/>
-        </section>
-        <section name="loopy_belief_propagation">
-          <param name="scheduling_type" value="priority"/>
-          <param name="convergence_threshold" value="1e-05"/>
-          <param name="dampening_lambda" value="0.001"/>
-          <param name="max_nr_iterations" value="2147483647"/>
-          <param name="p_norm_inference" value="1.0"/>
-        </section>
-        <section name="param_optimize">
-          <param name="aucweight" value="0.3"/>
-          <param name="conservative_fdr" value="true"/>
-          <param name="regularized_fdr" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="conservative_fdr" value="true"/>
-        <param name="min_psms_extreme_probability" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_2_input.consensusXML"/>
-      <output name="out" file="Epifany_3_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="protein_fdr" value="false"/>
-      <param name="greedy_group_resolution" value="none"/>
-      <param name="max_psms_extreme_probability" value="1.0"/>
-      <section name="algorithm">
-        <param name="psm_probability_cutoff" value="0.001"/>
-        <param name="top_PSMs" value="1"/>
-        <param name="keep_best_PSM_only" value="false"/>
-        <param name="update_PSM_probabilities" value="true"/>
-        <param name="user_defined_priors" value="false"/>
-        <param name="annotate_group_probabilities" value="true"/>
-        <param name="use_ids_outside_features" value="false"/>
-        <section name="model_parameters">
-          <param name="prot_prior" value="0.7"/>
-          <param name="pep_emission" value="0.1"/>
-          <param name="pep_spurious_emission" value="0.001"/>
-          <param name="pep_prior" value="0.1"/>
-          <param name="regularize" value="false"/>
-          <param name="extended_model" value="false"/>
-        </section>
-        <section name="loopy_belief_propagation">
-          <param name="scheduling_type" value="priority"/>
-          <param name="convergence_threshold" value="1e-05"/>
-          <param name="dampening_lambda" value="0.001"/>
-          <param name="max_nr_iterations" value="2147483647"/>
-          <param name="p_norm_inference" value="1.0"/>
-        </section>
-        <section name="param_optimize">
-          <param name="aucweight" value="0.3"/>
-          <param name="conservative_fdr" value="true"/>
-          <param name="regularized_fdr" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ERPairFinder">
-</xml>
-  <xml name="autotest_ExternalCalibration">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="offset" value="-5.5"/>
-      <param name="slope" value="0.0001"/>
-      <param name="power" value="0.0"/>
-      <param name="ms_level" value="1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="offset" value="-5.5"/>
-      <param name="slope" value="0.0001"/>
-      <param name="power" value="0.0"/>
-      <param name="ms_level" value="2"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FalseDiscoveryRate">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="true"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="true"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="true"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="false"/>
-      <param name="protein" value="true"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="true"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="true"/>
-      <param name="protein" value="false"/>
-      <section name="FDR">
-        <param name="PSM" value="0.05"/>
-        <param name="protein" value="1.0"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
-      <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="PSM" value="false"/>
-      <param name="protein" value="true"/>
-      <section name="FDR">
-        <param name="PSM" value="1.0"/>
-        <param name="protein" value="0.3"/>
-        <section name="cleanup">
-          <param name="remove_proteins_without_psms" value="true"/>
-          <param name="remove_psms_without_proteins" value="true"/>
-          <param name="remove_spectra_without_psms" value="true"/>
-        </section>
-      </section>
-      <section name="algorithm">
-        <param name="no_qvalues" value="false"/>
-        <param name="use_all_hits" value="false"/>
-        <param name="split_charge_variants" value="false"/>
-        <param name="treat_runs_separately" value="false"/>
-        <param name="add_decoy_peptides" value="false"/>
-        <param name="add_decoy_proteins" value="false"/>
-        <param name="conservative" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderCentroided">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-        <param name="pseudo_rt_shift" value="500.0"/>
-      </conditional>
-      <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
-      <output name="out" file="FeatureFinderCentroided_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="intensity">
-          <param name="bins" value="1"/>
-        </section>
-        <section name="mass_trace">
-          <param name="mz_tolerance" value="0.02"/>
-          <param name="min_spectra" value="14"/>
-          <param name="max_missing" value="1"/>
-          <param name="slope_bound" value="0.1"/>
-        </section>
-        <section name="isotopic_pattern">
-          <param name="charge_low" value="2"/>
-          <param name="charge_high" value="2"/>
-          <param name="mz_tolerance" value="0.02"/>
-          <param name="intensity_percentage" value="10.0"/>
-          <param name="intensity_percentage_optional" value="0.1"/>
-          <param name="optional_fit_improvement" value="2.0"/>
-          <param name="mass_window_width" value="100.0"/>
-          <param name="abundance_12C" value="98.93"/>
-          <param name="abundance_14N" value="99.632"/>
-        </section>
-        <section name="seed">
-          <param name="min_score" value="0.8"/>
-        </section>
-        <section name="fit">
-          <param name="max_iterations" value="500"/>
-        </section>
-        <section name="feature">
-          <param name="min_score" value="0.7"/>
-          <param name="min_isotope_fit" value="0.8"/>
-          <param name="min_trace_score" value="0.5"/>
-          <param name="min_rt_span" value="0.333"/>
-          <param name="max_rt_span" value="2.5"/>
-          <param name="rt_shape" value="symmetric"/>
-          <param name="max_intersection" value="0.35"/>
-          <param name="reported_mz" value="monoisotopic"/>
-        </section>
-        <section name="user-seed">
-          <param name="rt_tolerance" value="5.0"/>
-          <param name="mz_tolerance" value="1.1"/>
-          <param name="min_score" value="0.5"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderIdentification">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
-      <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="batch_size" value="1000"/>
-        <param name="mz_window" value="0.1"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_quantile" value="0.95"/>
-        <param name="rt_window" value="0.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="60.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-        <param name="mapping_tolerance" value="0.0"/>
-      </section>
-      <section name="svm">
-        <param name="samples" value="0"/>
-        <param name="no_selection" value="false"/>
-        <param name="kernel" value="RBF"/>
-        <param name="xval" value="5"/>
-        <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
-        <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
-        <param name="epsilon" value="0.001"/>
-        <param name="cache_size" value="100.0"/>
-        <param name="no_shrinking" value="false"/>
-        <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
-        <param name="min_prob" value="0.0"/>
-      </section>
-      <section name="model">
-        <param name="type" value="none"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
-        <param name="each_trace" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderIdentification_1_input.mzML"/>
-      <param name="id" value="FeatureFinderIdentification_1_input.idXML"/>
-      <output name="out" file="FeatureFinderIdentification_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="batch_size" value="1000"/>
-        <param name="mz_window" value="0.1"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_quantile" value="0.95"/>
-        <param name="rt_window" value="0.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="60.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-        <param name="mapping_tolerance" value="0.0"/>
-      </section>
-      <section name="svm">
-        <param name="samples" value="0"/>
-        <param name="no_selection" value="false"/>
-        <param name="kernel" value="RBF"/>
-        <param name="xval" value="5"/>
-        <param name="log2_C" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0"/>
-        <param name="log2_gamma" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0"/>
-        <param name="epsilon" value="0.001"/>
-        <param name="cache_size" value="100.0"/>
-        <param name="no_shrinking" value="false"/>
-        <param name="predictors" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score"/>
-        <param name="min_prob" value="0.0"/>
-      </section>
-      <section name="model">
-        <param name="type" value="symmetric"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
-        <param name="each_trace" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderIsotopeWavelet">
-</xml>
-  <xml name="autotest_FeatureFinderMetaboIdent">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetaboIdent_1_input.mzML"/>
-      <param name="id" value="FeatureFinderMetaboIdent_1_input.tsv" ftype="tabular"/>
-      <output name="out" file="FeatureFinderMetaboIdent_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="extract">
-        <param name="mz_window" value="5.0"/>
-        <param name="n_isotopes" value="2"/>
-        <param name="isotope_pmin" value="0.0"/>
-        <param name="rt_window" value="20.0"/>
-      </section>
-      <section name="detect">
-        <param name="peak_width" value="3.0"/>
-        <param name="min_peak_width" value="0.2"/>
-        <param name="signal_to_noise" value="0.8"/>
-      </section>
-      <section name="model">
-        <param name="type" value="symmetric"/>
-        <param name="add_zeros" value="0.2"/>
-        <param name="unweighted_fit" value="false"/>
-        <param name="no_imputation" value="false"/>
-        <param name="each_trace" value="false"/>
-        <section name="check">
-          <param name="min_area" value="1.0"/>
-          <param name="boundaries" value="0.5"/>
-          <param name="width" value="10.0"/>
-          <param name="asymmetry" value="10.0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderMetabo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="300.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="false"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="100.0"/>
-          <param name="chrom_peak_snr" value="0.0"/>
-          <param name="chrom_fwhm" value="100.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="5.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="median"/>
-          <param name="trace_termination_criterion" value="sample_rate"/>
-          <param name="trace_termination_outliers" value="2"/>
-          <param name="min_sample_rate" value="0.01"/>
-          <param name="min_trace_length" value="30.0"/>
-          <param name="max_trace_length" value="3000.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="false"/>
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="10.0"/>
-          <param name="max_fwhm" value="80.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="4.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="false"/>
-          <param name="isotope_filtering_model" value="none"/>
-          <param name="mz_scoring_13C" value="false"/>
-          <param name="use_smoothed_intensities" value="false"/>
-          <param name="report_convex_hulls" value="true"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="5.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="-1.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="fixed"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="none"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="true"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="5.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="-1.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="fixed"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="none"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="true"/>
-          <param name="remove_single_traces" value="true"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="max_height"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="300.0"/>
-        </section>
-        <section name="epd">
-          <param name="enabled" value="true"/>
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-        </section>
-        <section name="ffm">
-          <param name="local_rt_range" value="10.0"/>
-          <param name="local_mz_range" value="6.5"/>
-          <param name="charge_lower_bound" value="1"/>
-          <param name="charge_upper_bound" value="3"/>
-          <param name="report_summed_ints" value="false"/>
-          <param name="enable_RT_filtering" value="true"/>
-          <param name="isotope_filtering_model" value="metabolites (5% RMS)"/>
-          <param name="mz_scoring_13C" value="true"/>
-          <param name="use_smoothed_intensities" value="true"/>
-          <param name="report_convex_hulls" value="false"/>
-          <param name="remove_single_traces" value="false"/>
-          <param name="mz_scoring_by_elements" value="false"/>
-          <param name="elements" value="CHNOPS"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderMRM">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMRM_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMRM_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="min_rt_distance" value="10.0"/>
-        <param name="min_num_peaks_per_feature" value="5"/>
-        <param name="min_signal_to_noise_ratio" value="2.0"/>
-        <param name="write_debug_files" value="false"/>
-        <param name="resample_traces" value="false"/>
-        <param name="write_debuginfo" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderMultiplex">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="90.0"/>
-        <param name="rt_band" value="10.0"/>
-        <param name="rt_min" value="5.0"/>
-        <param name="mz_tolerance" value="40.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10.0"/>
-        <param name="peptide_similarity" value="0.8"/>
-        <param name="averagine_similarity" value="0.75"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Lys8,Arg10]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="40.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[]"/>
-        <param name="charge" value="5:15"/>
-        <param name="isotopes_per_peptide" value="5:10"/>
-        <param name="rt_typical" value="45.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="200.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="RNA"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[]"/>
-        <param name="charge" value="5:15"/>
-        <param name="isotopes_per_peptide" value="5:10"/>
-        <param name="rt_typical" value="45.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="200.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="DNA"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="charge" value="1:5"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="3.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10000000.0"/>
-        <param name="peptide_similarity" value="0.95"/>
-        <param name="averagine_similarity" value="0.8"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="spectrum_type" value="profile"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="charge" value="1:5"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="3.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10000000.0"/>
-        <param name="peptide_similarity" value="0.95"/>
-        <param name="averagine_similarity" value="0.8"/>
-        <param name="averagine_similarity_scaling" value="1.0"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="spectrum_type" value="profile"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Dimethyl4]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="40.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="2.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.75"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="31.0094"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
-        <param name="charge" value="1:7"/>
-        <param name="isotopes_per_peptide" value="3:8"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="3.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10.0"/>
-        <param name="peptide_similarity" value="0.2"/>
-        <param name="averagine_similarity" value="0.25"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="4"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="true"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[0][6.03705]"/>
-        <param name="charge" value="2:8"/>
-        <param name="isotopes_per_peptide" value="3:8"/>
-        <param name="rt_typical" value="40.0"/>
-        <param name="rt_band" value="0.0"/>
-        <param name="rt_min" value="4.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.4"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="centroid"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="charge" value="1:7"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="50.0"/>
-        <param name="rt_band" value="5.0"/>
-        <param name="rt_min" value="8.0"/>
-        <param name="mz_tolerance" value="6.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="10.0"/>
-        <param name="peptide_similarity" value="0.4"/>
-        <param name="averagine_similarity" value="0.5"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="spectrum_type" value="profile"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="true"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
-      <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="labels" value="[]"/>
-        <param name="charge" value="1:4"/>
-        <param name="isotopes_per_peptide" value="3:6"/>
-        <param name="rt_typical" value="1e-05"/>
-        <param name="rt_band" value="0.0"/>
-        <param name="rt_min" value="0.0"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_unit" value="ppm"/>
-        <param name="intensity_cutoff" value="1000.0"/>
-        <param name="peptide_similarity" value="0.5"/>
-        <param name="averagine_similarity" value="0.7"/>
-        <param name="averagine_similarity_scaling" value="0.95"/>
-        <param name="missed_cleavages" value="0"/>
-        <param name="spectrum_type" value="automatic"/>
-        <param name="averagine_type" value="peptide"/>
-        <param name="knock_out" value="false"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureFinderSuperHirn">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderSuperHirn_input_1.mzML"/>
-      <output name="out" file="FeatureFinderSuperHirn_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="centroiding">
-          <param name="active" value="false"/>
-          <param name="window_width" value="5"/>
-          <param name="absolute_isotope_mass_precision" value="0.01"/>
-          <param name="relative_isotope_mass_precision" value="10.0"/>
-          <param name="minimal_peak_height" value="0.0"/>
-          <param name="min_ms_signal_intensity" value="50.0"/>
-        </section>
-        <section name="ms1">
-          <param name="precursor_detection_scan_levels" value="1"/>
-          <param name="max_inter_scan_distance" value="0"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="intensity_threshold" value="1000.0"/>
-          <param name="max_inter_scan_rt_distance" value="0.1"/>
-          <param name="min_nb_cluster_members" value="4"/>
-          <param name="detectable_isotope_factor" value="0.05"/>
-          <param name="intensity_cv" value="0.9"/>
-          <param name="retention_time_tolerance" value="0.5"/>
-          <param name="mz_tolerance" value="0.0"/>
-        </section>
-        <section name="ms1_feature_merger">
-          <param name="active" value="true"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="initial_apex_tr_tolerance" value="5.0"/>
-          <param name="feature_merging_tr_tolerance" value="1.0"/>
-          <param name="intensity_variation_percentage" value="25.0"/>
-          <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
-        </section>
-        <section name="ms1_feature_selection_options">
-          <param name="start_elution_window" value="0.0"/>
-          <param name="end_elution_window" value="180.0"/>
-          <param name="mz_range_min" value="0.0"/>
-          <param name="mz_range_max" value="2000.0"/>
-          <param name="chrg_range_min" value="1"/>
-          <param name="chrg_range_max" value="5"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureFinderSuperHirn_input_2.mzML"/>
-      <output name="out" file="FeatureFinderSuperHirn_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="centroiding">
-          <param name="active" value="true"/>
-          <param name="window_width" value="5"/>
-          <param name="absolute_isotope_mass_precision" value="0.01"/>
-          <param name="relative_isotope_mass_precision" value="10.0"/>
-          <param name="minimal_peak_height" value="0.0"/>
-          <param name="min_ms_signal_intensity" value="50.0"/>
-        </section>
-        <section name="ms1">
-          <param name="precursor_detection_scan_levels" value="1"/>
-          <param name="max_inter_scan_distance" value="0"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="intensity_threshold" value="1000.0"/>
-          <param name="max_inter_scan_rt_distance" value="0.1"/>
-          <param name="min_nb_cluster_members" value="4"/>
-          <param name="detectable_isotope_factor" value="0.05"/>
-          <param name="intensity_cv" value="0.9"/>
-          <param name="retention_time_tolerance" value="0.5"/>
-          <param name="mz_tolerance" value="0.0"/>
-        </section>
-        <section name="ms1_feature_merger">
-          <param name="active" value="true"/>
-          <param name="tr_resolution" value="0.01"/>
-          <param name="initial_apex_tr_tolerance" value="5.0"/>
-          <param name="feature_merging_tr_tolerance" value="1.0"/>
-          <param name="intensity_variation_percentage" value="25.0"/>
-          <param name="ppm_tolerance_for_mz_clustering" value="10.0"/>
-        </section>
-        <section name="ms1_feature_selection_options">
-          <param name="start_elution_window" value="0.0"/>
-          <param name="end_elution_window" value="180.0"/>
-          <param name="mz_range_min" value="0.0"/>
-          <param name="mz_range_max" value="2000.0"/>
-          <param name="chrg_range_min" value="1"/>
-          <param name="chrg_range_max" value="5"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerLabeled">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="rt_estimate" value="false"/>
-        <param name="rt_pair_dist" value="-1.0"/>
-        <param name="rt_dev_low" value="0.4"/>
-        <param name="rt_dev_high" value="0.4"/>
-        <param name="mz_pair_dists" value="8.0"/>
-        <param name="mz_dev" value="0.1"/>
-        <param name="mrm" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
-      <output name="out" file="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="rt_estimate" value="true"/>
-        <param name="rt_pair_dist" value="-121.0382"/>
-        <param name="rt_dev_low" value="123.3965"/>
-        <param name="rt_dev_high" value="123.3965"/>
-        <param name="mz_pair_dists" value="4.0"/>
-        <param name="mz_dev" value="0.1"/>
-        <param name="mrm" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerUnlabeledKD">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="Da"/>
-        <param name="nr_partitions" value="1"/>
-        <section name="warp">
-          <param name="enabled" value="false"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_1_output.consensusXML,FeatureLinkerUnlabeledKD_1_output_2.consensusXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="true"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="Da"/>
-        <param name="nr_partitions" value="99999"/>
-        <section name="warp">
-          <param name="enabled" value="false"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="Da"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="false"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="0.3"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="Identical"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="With_charge_zero"/>
-          <param name="adduct_merging" value="Any"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="Any"/>
-          <param name="adduct_merging" value="With_unknown_adducts"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledKD_dc_input1.featureXML,FeatureLinkerUnlabeledKD_dc_input2.featureXML,FeatureLinkerUnlabeledKD_dc_input3.featureXML,FeatureLinkerUnlabeledKD_dc_input1_2.featureXML,FeatureLinkerUnlabeledKD_dc_input2_2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledKD_7_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="mz_unit" value="ppm"/>
-        <param name="nr_partitions" value="100"/>
-        <section name="warp">
-          <param name="enabled" value="true"/>
-          <param name="rt_tol" value="100.0"/>
-          <param name="mz_tol" value="5.0"/>
-          <param name="max_pairwise_log_fc" value="0.5"/>
-          <param name="min_rel_cc_size" value="0.5"/>
-          <param name="max_nr_conflicts" value="0"/>
-        </section>
-        <section name="link">
-          <param name="rt_tol" value="30.0"/>
-          <param name="mz_tol" value="10.0"/>
-          <param name="charge_merging" value="Any"/>
-          <param name="adduct_merging" value="Identical"/>
-        </section>
-        <section name="distance_RT">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-          <param name="log_transform" value="enabled"/>
-        </section>
-        <section name="LOWESS">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerUnlabeledQT">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_1_output.consensusXML,FeatureLinkerUnlabeledQT_1_output_2.consensusXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="true"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_3_input1.featureXML,FeatureLinkerUnlabeledQT_3_input2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="99999"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="true"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_5_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="false"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeledQT_5_input1.featureXML,FeatureLinkerUnlabeledQT_5_input2.featureXML,FeatureLinkerUnlabeledQT_5_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeledQT_6_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="use_identifications" value="true"/>
-        <param name="nr_partitions" value="100"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FeatureLinkerUnlabeled">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="2.0"/>
-        <param name="use_identifications" value="false"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.5"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_2_input1.featureXML,FeatureLinkerUnlabeled_2_input2.featureXML,FeatureLinkerUnlabeled_2_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="2.0"/>
-        <param name="use_identifications" value="false"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="100.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.5"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_3_input1.featureXML,FeatureLinkerUnlabeled_3_input2.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="1.5"/>
-        <param name="use_identifications" value="false"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="30.0"/>
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.3"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FeatureLinkerUnlabeled_1_input1.featureXML,FeatureLinkerUnlabeled_1_input2.featureXML,FeatureLinkerUnlabeled_1_input3.featureXML"/>
-      <output name="out" file="FeatureLinkerUnlabeled_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="keep_subelements" value="false"/>
-      <section name="algorithm">
-        <param name="second_nearest_gap" value="2.0"/>
-        <param name="use_identifications" value="true"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="ignore_adduct" value="true"/>
-        <section name="distance_RT">
-          <param name="max_difference" value="200.0"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_MZ">
-          <param name="max_difference" value="0.5"/>
-          <param name="unit" value="Da"/>
-          <param name="exponent" value="2.0"/>
-          <param name="weight" value="1.0"/>
-        </section>
-        <section name="distance_intensity">
-          <param name="exponent" value="1.0"/>
-          <param name="weight" value="0.0"/>
-          <param name="log_transform" value="disabled"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FFEval">
-</xml>
-  <xml name="autotest_FidoAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="true"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="true"/>
-      <param name="group_level" value="true"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_4_input.idXML"/>
-      <output name="out" file="FidoAdapter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_5_input.idXML"/>
-      <output name="out" file="FidoAdapter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="true"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.0"/>
-        <param name="peptide" value="0.0"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_zero_group" value="false"/>
-        <param name="accuracy" value=""/>
-        <param name="log2_states_precalc" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FidoAdapter_1_input.idXML"/>
-      <output name="out" file="FidoAdapter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="separate_runs" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="no_cleanup" value="false"/>
-      <param name="all_PSMs" value="false"/>
-      <param name="group_level" value="false"/>
-      <param name="log2_states" value="0"/>
-      <section name="prob">
-        <param name="protein" value="0.9"/>
-        <param name="peptide" value="0.01"/>
-        <param name="spurious" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_1_input.mzData"/>
-      <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_2_input.someInputDTA2D"/>
-      <output name="out" file="FileConverter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_3_input.featureXML"/>
-      <output name="out" file="FileConverter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_4_input.mzXML"/>
-      <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_5_input.mzML"/>
-      <output name="out" file="FileConverter_5_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_6_input.mzML"/>
-      <output name="out" file="FileConverter_6_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_7_input.consensusXML"/>
-      <output name="out" file="FileConverter_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_8_input.mzML"/>
-      <output name="out" file="FileConverter_8_output.mzData" compare="sim_size" delta="5700" ftype="mzdata"/>
-      <param name="out_type" value="mzData"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_9_input.consensusXML"/>
-      <output name="out" file="FileConverter_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_11_input.peplist"/>
-      <output name="out" file="FileConverter_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_12_input.peptides.tsv" ftype="tabular"/>
-      <output name="out" file="FileConverter_12_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_13_input.peptides.kroenik"/>
-      <output name="out" file="FileConverter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_9_output.featureXML"/>
-      <output name="out" file="FileConverter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_10_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_15_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_16_input.edta" ftype="edta"/>
-      <output name="out" file="FileConverter_16_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_17_input.consensusXML"/>
-      <output name="out" file="FileConverter_17.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="out_type" value="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_17_input.consensusXML"/>
-      <output name="out" file="FileConverter_17_output.ibspectra.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="out_type" value="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_19_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_20_input.featureXML"/>
-      <output name="out" file="FileConverter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_4_input.mzXML"/>
-      <output name="out" file="FileConverter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_23_input.mzML"/>
-      <output name="out" file="FileConverter_23_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="true"/>
-        <param name="lossy_mass_accuracy" value="0.0001"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_24_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="true"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="true"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileConverter_26_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="true"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_26_output.mzXML"/>
-      <output name="out" file="FileConverter_26-2_output.mzXML" compare="sim_size" delta="5700" ftype="mzxml"/>
-      <param name="out_type" value="mzXML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="true"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_27_input.mzML"/>
-      <output name="out" file="FileConverter_27_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="true"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_28_input.mzML"/>
-      <output name="out" file="FileConverter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="true"/>
-        <param name="lossy_mass_accuracy" value="1e-05"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <output name="out" file="FileConverter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_29_output.mzML"/>
-      <output name="out" file="FileConverter_29.back.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="multiple"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_30_input.mzML"/>
-      <output name="out" file="FileConverter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="single"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_30_output.mzML"/>
-      <output name="out" file="FileConverter_31_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileConverter_32_input.mzML"/>
-      <output name="out" file="FileConverter_32_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="UID_postprocessing" value="ensure"/>
-        <param name="TIC_DTA2D" value="false"/>
-        <param name="MGF_compact" value="false"/>
-        <param name="force_MaxQuant_compatibility" value="false"/>
-        <param name="convert_to_chromatograms" value="false"/>
-        <param name="force_TPP_compatibility" value="false"/>
-        <param name="change_im_format" value="none"/>
-        <param name="write_scan_index" value="true"/>
-        <param name="lossy_compression" value="false"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="no_peak_picking" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ginkgotoxin-ms-switching.raw"/>
-      <output name="out" file="ginkgotoxin-ms-switching_out_tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":30"/>
-      <param name="mz" value=":1000"/>
-      <param name="int" value=":20000"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value="30:"/>
-      <param name="mz" value="1000:"/>
-      <param name="int" value="100:"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_4_input.mzML"/>
-      <output name="out" file="FileFilter_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="true"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_5_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="rt" value=":1000"/>
-      <param name="mz" value=":480"/>
-      <param name="int" value=":79000"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":0.6"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":3"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_5_input.featureXML"/>
-      <output name="out" file="FileFilter_6_out.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="rt" value="1000:"/>
-      <param name="mz" value="440:"/>
-      <param name="int" value="70000:"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value="0.51:"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value="3:"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_7_input.mzML"/>
-      <output name="out" file="FileFilter_7_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value="7000:"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_8_input.consensusXML"/>
-      <output name="out" file="FileFilter_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="rt" value="600:1400"/>
-      <param name="mz" value="700:2300"/>
-      <param name="int" value="1100:6000"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_9_input.mzML"/>
-      <output name="out" file="FileFilter_9_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value="SelectedIonMonitoring"/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_10_input.mzML"/>
-      <output name="out" file="FileFilter_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value="Collision-induced dissociation"/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_11_input.mzML"/>
-      <output name="out" file="FileFilter_11_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value="Plasma desorption"/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_12_input.mzML"/>
-      <output name="out" file="FileFilter_12_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="true"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_13_input.consensusXML"/>
-      <output name="out" file="FileFilter_13_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featureXML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value="2"/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_14_input.consensusXML"/>
-      <output name="out" file="FileFilter_14_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusXML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value="0 2"/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value="3000:4000"/>
-      <param name="mz" value="400:600"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_17_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value="3000:4000"/>
-      <param name="mz" value="400:600"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="true"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_18_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;Oxidation&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_18_input.consensusXML"/>
-      <output name="out" file="FileFilter_19_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value="3000:4000"/>
-      <param name="mz" value="400:600"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="true"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value="&quot;YDL217C&quot;"/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_15_input.featureXML"/>
-      <output name="out" file="FileFilter_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="true"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="true"/>
-        <param name="remove_unassigned_ids" value="true"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value="&quot;distinct_charges&quot; &quot;gt&quot; &quot;1,2&quot;"/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_22_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value="&quot;distinct_charges_size&quot; &quot;gt&quot; &quot;2&quot;"/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_22_input.consensusXML"/>
-      <output name="out" file="FileFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="out_type" value="consensusxml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value="&quot;DOESNOTEXIST&quot; &quot;lt&quot; &quot;whatever&quot;"/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="blacklist" value="FileFilter_25_input.idXML"/>
-        <param name="rt" value="1.0"/>
-        <param name="mz" value="0.05"/>
-        <param name="blacklist_imperfect" value="true"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_25_input.mzML.gz"/>
-      <output name="out" file="FileFilter_25_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="blacklist" value="FileFilter_25_input.idXML"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="true"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_28_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_29_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_28_input.mzML.gz"/>
-      <output name="out" file="FileFilter_30_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value="832:836"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_31_remove_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":2"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_32_select_collision_energy.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":2"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_33_remove_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":35"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_31_34_input.mzML"/>
-      <output name="out" file="FileFilter_34_select_isolation_window.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":35"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_35_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_36_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="false"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_37_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="linear"/>
-          <param name="lossy_mass_accuracy" value="0.0001"/>
-          <param name="intensity" value="slof"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output name="out" file="FileFilter_38_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="linear"/>
-          <param name="lossy_mass_accuracy" value="0.0001"/>
-          <param name="intensity" value="pic"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_40_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value="positive"/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_41_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value="negative"/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_40_input.mzML"/>
-      <output name="out" file="FileFilter_42_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_43_input.mzML"/>
-      <output name="out" file="FileFilter_43.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_43.tmp.mzML"/>
-      <output name="out" file="FileFilter_43.dummy.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_44_input.mzML"/>
-      <output name="out" file="FileFilter_44_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzML"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_45_input.featureXML"/>
-      <output name="out" file="FileFilter_45_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_46_input.featureXML"/>
-      <output name="out" file="FileFilter_46_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value="&quot;YSFS&quot; &quot;STLIPPPSK(Label:13C(6)15N(2))&quot;"/>
-        <param name="sequence_comparison_method" value="exact"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_47_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="file" value="FileFilter_47_input_select.mzML"/>
-          <param name="similarity_threshold" value="0.9"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_47_input.mzML"/>
-      <output name="out" file="FileFilter_48_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="false"/>
-        <section name="numpress">
-          <param name="masstime" value="none"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="none"/>
-          <param name="float_da" value="none"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="file" value="FileFilter_47_input_select.mzML"/>
-          <param name="similarity_threshold" value="0.9"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="false"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_49_input.mzML"/>
-      <output name="out" file="FileFilter_49_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="rt" value=":"/>
-      <param name="mz" value=":"/>
-      <param name="int" value=":"/>
-      <param name="sort" value="false"/>
-      <section name="peak_options">
-        <param name="sn" value="0.0"/>
-        <param name="rm_pc_charge" value=""/>
-        <param name="pc_mz_range" value=":"/>
-        <param name="pc_mz_list" value=""/>
-        <param name="level" value="1 2 3"/>
-        <param name="sort_peaks" value="false"/>
-        <param name="no_chromatograms" value="false"/>
-        <param name="remove_chromatograms" value="false"/>
-        <param name="remove_empty" value="false"/>
-        <param name="mz_precision" value="64"/>
-        <param name="int_precision" value="32"/>
-        <param name="indexed_file" value="true"/>
-        <param name="zlib_compression" value="true"/>
-        <section name="numpress">
-          <param name="masstime" value="linear"/>
-          <param name="lossy_mass_accuracy" value="-1.0"/>
-          <param name="intensity" value="pic"/>
-          <param name="float_da" value="slof"/>
-        </section>
-      </section>
-      <section name="spectra">
-        <param name="remove_zoom" value="false"/>
-        <param name="remove_mode" value=""/>
-        <param name="remove_activation" value=""/>
-        <param name="remove_collision_energy" value=":"/>
-        <param name="remove_isolation_window_width" value=":"/>
-        <param name="select_zoom" value="false"/>
-        <param name="select_mode" value=""/>
-        <param name="select_activation" value=""/>
-        <param name="select_collision_energy" value=":"/>
-        <param name="select_isolation_window_width" value=":"/>
-        <param name="select_polarity" value=""/>
-        <section name="blackorwhitelist">
-          <param name="similarity_threshold" value="-1.0"/>
-          <param name="rt" value="0.01"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-          <param name="blacklist" value="true"/>
-        </section>
-      </section>
-      <section name="feature">
-        <param name="q" value=":"/>
-      </section>
-      <section name="consensus">
-        <param name="map" value=""/>
-        <param name="map_and" value="false"/>
-        <section name="blackorwhitelist">
-          <param name="blacklist" value="true"/>
-          <param name="maps" value=""/>
-          <param name="rt" value="60.0"/>
-          <param name="mz" value="0.01"/>
-          <param name="use_ppm_tolerance" value="false"/>
-        </section>
-      </section>
-      <section name="f_and_c">
-        <param name="charge" value=":"/>
-        <param name="size" value=":"/>
-        <param name="remove_meta" value=""/>
-      </section>
-      <section name="id">
-        <param name="remove_clashes" value="false"/>
-        <param name="keep_best_score_id" value="false"/>
-        <param name="sequences_whitelist" value=""/>
-        <param name="sequence_comparison_method" value="substring"/>
-        <param name="accessions_whitelist" value=""/>
-        <param name="remove_annotated_features" value="false"/>
-        <param name="remove_unannotated_features" value="false"/>
-        <param name="remove_unassigned_ids" value="false"/>
-        <param name="rt" value="0.1"/>
-        <param name="mz" value="0.001"/>
-        <param name="blacklist_imperfect" value="false"/>
-      </section>
-      <section name="algorithm">
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileInfo">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_1_input.dta" ftype="dta"/>
-      <output name="out" file="FileInfo_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_2_input.dta2d" ftype="dta2d"/>
-      <output name="out" file="FileInfo_2_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_3_input.featureXML"/>
-      <output name="out" file="FileInfo_3_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="true"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_4_input.mzXML"/>
-      <output name="out" file="FileInfo_4_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_5_input.mzDat"/>
-      <output name="out" file="FileInfo_5_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="false"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_6_input.mzData"/>
-      <output name="out" file="FileInfo_6_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="true"/>
-      <param name="d" value="true"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_7_input.consensusXML"/>
-      <output name="out" file="FileInfo_7_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="true"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_9_input.mzML"/>
-      <output name="out" file="FileInfo_9_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="true"/>
-      <param name="p" value="true"/>
-      <param name="s" value="true"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_10_input.idXML"/>
-      <output name="out" file="FileInfo_10_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_12_input.mzML"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_13_input.consensusXML"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_14_input.mzid"/>
-      <output name="out" file="FileInfo_14_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="true"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_15_input.mzid"/>
-      <output name="out" file="FileInfo_15_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="true"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_16_input.trafoXML"/>
-      <output name="out" file="FileInfo_16_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_17_input.fasta"/>
-      <output name="out" file="FileInfo_17_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileInfo_18_input.fasta"/>
-      <output name="out" file="FileInfo_18_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="m" value="false"/>
-      <param name="p" value="false"/>
-      <param name="s" value="false"/>
-      <param name="d" value="false"/>
-      <param name="c" value="false"/>
-      <param name="v" value="false"/>
-      <param name="i" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FileMerger">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value="5.0 10.0"/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="true"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="true"/>
-        <param name="ms_level" value="2"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/>
-      <param name="out_type" value="featureXML"/>
-      <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
-      <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/>
-      <param name="out_type" value="traML"/>
-      <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/>
-      <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_rows"/>
-      <section name="rt_concat">
-        <param name="gap" value="10.0"/>
-      </section>
-      <output_collection name="rt_concat_trafo_out" count="2"/>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
-      <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="append_method" value="append_cols"/>
-      <section name="rt_concat">
-        <param name="gap" value="0.0"/>
-      </section>
-      <section name="raw">
-        <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
-        <param name="rt_filename" value="false"/>
-        <param name="ms_level" value="0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_FuzzyDiff">
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
-        <param name="matched_whitelist" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
-      <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
-      <param name="ratio" value="1.01"/>
-      <param name="absdiff" value="0.01"/>
-      <param name="verbose" value="1"/>
-      <param name="tab_width" value="8"/>
-      <param name="first_column" value="1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_GNPSExport">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_single.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
-      <output name="out" file="GNPSExport_1_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="full_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_single.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML"/>
-      <output name="out" file="GNPSExport_2_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="merged_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
-      <output name="out" file="GNPSExport_3_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="full_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="GNPSExport_merged.consensusXML"/>
-      <param name="in_mzml" value="GNPSExport_mz1.mzML,GNPSExport_mz2.mzML"/>
-      <output name="out" file="GNPSExport_4_out.mgf" compare="sim_size" delta="5700" ftype="mgf"/>
-      <param name="output_type" value="full_spectra"/>
-      <param name="precursor_mz_tolerance" value="0.0001"/>
-      <param name="precursor_rt_tolerance" value="5.0"/>
-      <section name="merged_spectra">
-        <param name="cos_similarity" value="0.95"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_HighResPrecursorMassCorrector">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="4"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="feature">
-        <param name="mz_tolerance" value="5.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="2"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.2"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDConflictResolver">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_1_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="resolve_between_features" value="off"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_2_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="resolve_between_features" value="off"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_3_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="resolve_between_features" value="off"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDConflictResolver_4_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="resolve_between_features" value="highest_intensity"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDExtractor">
-</xml>
-  <xml name="autotest_IDFileConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
-      <output name="out" file="IDFileConverter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PepXMLFile_test.pepxml"/>
-      <output name="out" file="IDFileConverter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="PepXMLFile_test.mzML"/>
-      <param name="mz_name" value="PepXMLFile_test"/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_3_input.protXML"/>
-      <output name="out" file="IDFileConverter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value="scan=(?&lt;SCAN&gt;\d+)"/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_1_input1.mascotXML"/>
-      <output name="out" file="IDFileConverter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_6_input1.pepXML"/>
-      <output name="out" file="IDFileConverter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDFileConverter_1_input2.mzML"/>
-      <param name="mz_name" value="F025589.dat.mzML"/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_7_input1.xml"/>
-      <output name="out" file="IDFileConverter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_8_input.mzid"/>
-      <output name="out" file="IDFileConverter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_9_input.idXML"/>
-      <output name="out" file="IDFileConverter_9_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <param name="out_type" value="mzid"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_10_input.pepXML"/>
-      <output name="out" file="IDFileConverter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_11_input.tsv" ftype="tabular"/>
-      <output name="out" file="IDFileConverter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="PEP"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_input.psms"/>
-      <output name="out" file="IDFileConverter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="score"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
-      <output name="out" file="IDFileConverter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="spectra.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_16_input.pepXML"/>
-      <output name="out" file="IDFileConverter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_17_input.idXML"/>
-      <output name="out" file="IDFileConverter_17_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_18_input.idXML"/>
-      <output name="out" file="IDFileConverter_18_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_19_input.idXML"/>
-      <output name="out" file="IDFileConverter_19_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_20_input.idXML"/>
-      <output name="out" file="IDFileConverter_20_output.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_21_input.idXML"/>
-      <output name="out" file="IDFileConverter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="IDMapper_4_input.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.01"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSGFPlusAdapter_1_out.mzid"/>
-      <output name="out" file="IDFileConverter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_file" value="spectra.mzML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_23_input.mzid"/>
-      <output name="out" file="IDFileConverter_23_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_24_input.pep.xml"/>
-      <output name="out" file="IDFileConverter_24_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_25_input.idXML"/>
-      <output name="out" file="IDFileConverter_25_output.pep.xml" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="out_type" value="pepXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_26_input.mzid"/>
-      <output name="out" file="IDFileConverter_26_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_27_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="-1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_28_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="true"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_29_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="true"/>
-        <param name="number_of_hits" value="2"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_27_input.idXML"/>
-      <output name="out" file="IDFileConverter_30_output.fasta" compare="sim_size" delta="5700" ftype="fasta"/>
-      <param name="out_type" value="FASTA"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_proteins_per_peptide" value="false"/>
-        <param name="scan_regex" value=""/>
-        <param name="no_spectra_data_override" value="false"/>
-        <param name="no_spectra_references_override" value="false"/>
-        <param name="add_ionmatch_annotation" value="0.0"/>
-        <param name="concatenate_peptides" value="false"/>
-        <param name="number_of_hits" value="1"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_31_input.mzid"/>
-      <output name="out" file="IDFileConverter_31_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="mz_name" value=""/>
-      <param name="peptideprophet_analyzed" value="false"/>
-      <param name="score_type" value="qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDFilter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_1_input.idXML"/>
-      <output name="out" file="IDFilter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="proteins" value="IDFilter_1_input.fas"/>
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_3_input.idXML"/>
-      <output name="out" file="IDFilter_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="peptides" value="IDFilter_3_2_input.idXML"/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_4_input.idXML"/>
-      <output name="out" file="IDFilter_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.08"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="32.0"/>
-        <param name="prot" value="25.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="32.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5b_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="25.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_5_input.idXML"/>
-      <output name="out" file="IDFilter_5c_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="true"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="25.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_6_input.idXML"/>
-      <output name="out" file="IDFilter_6_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="2"/>
-        <param name="n_protein_hits" value="10"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="true"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_7_input.idXML"/>
-      <output name="out" file="IDFilter_7_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_8_input.idXML"/>
-      <output name="out" file="IDFilter_8_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value="200:350"/>
-        <param name="mz" value="999:1000"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_9_input.idXML"/>
-      <output name="out" file="IDFilter_9_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.05"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_10_input.idXML"/>
-      <output name="out" file="IDFilter_10_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="true"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.3"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_11_input.idXML"/>
-      <output name="out" file="IDFilter_11_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="true"/>
-      <param name="delete_unreferenced_peptide_hits" value="true"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_12_input.idXML"/>
-      <output name="out" file="IDFilter_12_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_12_input.fasta"/>
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_13_input.idXML"/>
-      <output name="out" file="IDFilter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_13_input.fasta"/>
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_14_input.idXML"/>
-      <output name="out" file="IDFilter_14_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_14_input.fasta"/>
-        <param name="enzyme" value="Trypsin/P"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_15_input.idXML"/>
-      <output name="out" file="IDFilter_15_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_15_input.fasta"/>
-        <param name="enzyme" value="Trypsin/P"/>
-        <param name="specificity" value="semi"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_16_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="fasta" value="IDFilter_16_input.fasta"/>
-        <param name="enzyme" value="Trypsin/P"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="methionine_cleavage" value="true"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_17_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":2"/>
-        <param name="enzyme" value="Lys-N"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_18_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value="2:"/>
-        <param name="enzyme" value="Lys-N"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_19_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value="1:3"/>
-        <param name="enzyme" value="Lys-N"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_missed_cleavages_input.idXML"/>
-      <output name="out" file="IDFilter_20_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value="1:0"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value="&quot;calcMZ&quot; &quot;gt&quot; &quot;750.0&quot;"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_21_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value="&quot;end&quot; &quot;ne&quot; &quot;23&quot;"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFilter_16_input.idXML"/>
-      <output name="out" file="IDFilter_22_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMapper_2_output.consensusXML"/>
-      <output name="out" file="IDFilter_23_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.0"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value="&quot;Q9HP81&quot;"/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="remove_duplicate_psm" value="false"/>
-        <param name="remove_peptide_hits_by_metavalue" value=""/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_3_out.consensusXML"/>
-      <output name="out" file="IDFilter_24_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="var_mods" value="false"/>
-      <param name="remove_shared_peptides" value="false"/>
-      <param name="keep_unreferenced_protein_hits" value="false"/>
-      <param name="remove_decoys" value="false"/>
-      <param name="delete_unreferenced_peptide_hits" value="false"/>
-      <section name="precursor">
-        <param name="rt" value=":"/>
-        <param name="mz" value=":"/>
-        <param name="length" value=":"/>
-        <param name="charge" value=":"/>
-      </section>
-      <section name="score">
-        <param name="pep" value="0.0"/>
-        <param name="prot" value="0.0"/>
-        <param name="protgroup" value="0.99"/>
-      </section>
-      <section name="whitelist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="blacklist">
-        <param name="protein_accessions" value=""/>
-        <param name="ignore_modifications" value="false"/>
-        <param name="modifications" value=""/>
-      </section>
-      <section name="in_silico_digestion">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="specificity" value="full"/>
-        <param name="missed_cleavages" value="-1"/>
-        <param name="methionine_cleavage" value="false"/>
-      </section>
-      <section name="missed_cleavages">
-        <param name="number_of_missed_cleavages" value=":"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="rt">
-        <param name="p_value" value="0.0"/>
-        <param name="p_value_1st_dim" value="0.0"/>
-      </section>
-      <section name="mz">
-        <param name="error" value="-1.0"/>
-        <param name="unit" value="ppm"/>
-      </section>
-      <section name="best">
-        <param name="n_peptide_hits" value="0"/>
-        <param name="n_protein_hits" value="0"/>
-        <param name="strict" value="false"/>
-        <param name="n_to_m_peptide_hits" value=":"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDMapper">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_1_input.idXML"/>
-      <param name="in" value="IDMapper_1_input.featureXML"/>
-      <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="5.0"/>
-      <param name="mz_tolerance" value="1.0"/>
-      <param name="mz_measure" value="Da"/>
-      <param name="mz_reference" value="precursor"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="false"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_2_input.idXML"/>
-      <param name="in" value="IDMapper_2_input.consensusXML"/>
-      <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="rt_tolerance" value="5.0"/>
-      <param name="mz_tolerance" value="1.0"/>
-      <param name="mz_measure" value="Da"/>
-      <param name="mz_reference" value="precursor"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_3_input.idXML"/>
-      <param name="in" value="IDMapper_3_input.featureXML"/>
-      <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="4.0"/>
-      <param name="mz_tolerance" value="3.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="precursor"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_4_input.idXML"/>
-      <param name="in" value="IDMapper_4_input.featureXML"/>
-      <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="10.0"/>
-      <param name="mz_tolerance" value="20.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_4_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="id" value="IDMapper_5_input.idXML"/>
-      <param name="in" value="IDMapper_5_input.featureXML"/>
-      <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="rt_tolerance" value="20.0"/>
-      <param name="mz_tolerance" value="10.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="false"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_5_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDMassAccuracy">
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="number_of_bins" value="10"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
-      <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="precursor_error_ppm" value="false"/>
-      <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="fragment_error_ppm" value="false"/>
-      <param name="fragment_mass_tolerance" value="0.5"/>
-      <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDMerger">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
-      <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="true"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
-      <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="true"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
-      <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
-      <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMerger_2_input1.idXML"/>
-      <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="add_to" value="IDMerger_5_input1.idXML"/>
-      <param name="annotate_file_origin" value="false"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
-      <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="annotate_file_origin" value="true"/>
-      <param name="pepxml_protxml" value="false"/>
-      <param name="merge_proteins_add_PSMs" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDPosteriorErrorProbability">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_Mascot_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_XTandem_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_OMSSA_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_OMSSA_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="true"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_XTandem_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_XTandem_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="true"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_Mascot_input2.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_Mascot_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="true"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_bad_data.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_bad_data_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="true"/>
-      <param name="prob_correct" value="false"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="fdr_for_targets_smaller" value="0.05"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDPosteriorErrorProbability_OMSSA_input.idXML"/>
-      <output name="out" file="IDPosteriorErrorProbability_prob_correct_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="split_charge" value="false"/>
-      <param name="top_hits_only" value="false"/>
-      <param name="ignore_bad_data" value="false"/>
-      <param name="prob_correct" value="true"/>
-      <section name="fit_algorithm">
-        <param name="number_of_bins" value="100"/>
-        <param name="incorrectly_assigned" value="Gumbel"/>
-        <param name="max_nr_iterations" value="1000"/>
-        <param name="neg_log_delta" value="6"/>
-        <param name="outlier_handling" value="ignore_iqr_outliers"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDRipper"/>
-  <xml name="autotest_IDRTCalibration">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDRTCalibration_1_input.idXML"/>
-      <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="calibrant_1_reference" value="0.1"/>
-      <param name="calibrant_2_reference" value="0.9"/>
-      <param name="calibrant_1_input" value="10.0"/>
-      <param name="calibrant_2_input" value="90.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="degenerated_empty.idXML"/>
-      <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="calibrant_1_reference" value="0.1"/>
-      <param name="calibrant_2_reference" value="0.9"/>
-      <param name="calibrant_1_input" value="10.0"/>
-      <param name="calibrant_2_input" value="90.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDScoreSwitcher">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDFileConverter_12_output.idXML"/>
-      <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="proteins" value="false"/>
-      <param name="new_score" value="Percolator_PEP"/>
-      <param name="new_score_orientation" value="lower_better"/>
-      <param name="new_score_type" value="Posterior Error Probability"/>
-      <param name="old_score" value="Percolator_qvalue"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDScoreSwitcher_2_input.idXML"/>
-      <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="proteins" value="true"/>
-      <param name="new_score" value="Posterior Probability_score"/>
-      <param name="new_score_orientation" value="higher_better"/>
-      <param name="new_score_type" value="Posterior Probability"/>
-      <param name="old_score" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IDSplitter">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMapper_1_output.featureXML"/>
-      <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_InternalCalibration">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
-      <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ppm_match_tolerance" value="25.0"/>
-      <param name="ms_level" value="1"/>
-      <param name="RT_chunking" value="-1.0"/>
-      <section name="cal">
-        <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
-        <param name="lock_require_mono" value="false"/>
-        <param name="lock_require_iso" value="false"/>
-        <param name="model_type" value="linear"/>
-      </section>
-      <section name="RANSAC">
-        <param name="enabled" value="true"/>
-        <param name="threshold" value="1.0"/>
-        <param name="pc_inliers" value="30"/>
-        <param name="iter" value="500"/>
-      </section>
-      <section name="goodness">
-        <param name="median" value="4.0"/>
-        <param name="MAD" value="2.0"/>
-      </section>
-      <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
-      <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ppm_match_tolerance" value="25.0"/>
-      <param name="ms_level" value="1 2 3"/>
-      <param name="RT_chunking" value="60.0"/>
-      <section name="cal">
-        <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
-        <param name="lock_require_mono" value="true"/>
-        <param name="lock_require_iso" value="false"/>
-        <param name="model_type" value="linear"/>
-      </section>
-      <section name="RANSAC">
-        <param name="enabled" value="false"/>
-        <param name="threshold" value="10.0"/>
-        <param name="pc_inliers" value="30"/>
-        <param name="iter" value="70"/>
-      </section>
-      <section name="goodness">
-        <param name="median" value="4.0"/>
-        <param name="MAD" value="2.0"/>
-      </section>
-      <section name="quality_control"/>
-      <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_IsobaricAnalyzer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="itraq4plex"/>
-      <param name="in" value="IsobaricAnalyzer_input_1.mzML"/>
-      <output name="out" file="IsobaricAnalyzer_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value=""/>
-        <param name="reporter_mass_shift" value="0.1"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value="l1"/>
-        <param name="channel_115_description" value="l2"/>
-        <param name="channel_116_description" value="l3"/>
-        <param name="channel_117_description" value="lung"/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="itraq4plex"/>
-      <param name="in" value="TMTTenPlexMethod_test.mzML"/>
-      <output name="out" file="TMTTenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value="High-energy collision-induced dissociation"/>
-        <param name="reporter_mass_shift" value="0.002"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/5.0/0.0&quot; &quot;0.0/0.2/4.6/0.0&quot; &quot;0.0/0.2/4.6/0.3&quot; &quot;0.0/0.9/4.7/0.2&quot; &quot;0.0/0.5/3.2/0.0&quot; &quot;0.0/0.7/3.3/0.0&quot; &quot;0.0/1.3/2.5/0.0&quot; &quot;0.0/1.2/2.8/2.7&quot; &quot;0.0/1.5/2.0/0.0&quot; &quot;0.0/1.5/1.9/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="itraq4plex"/>
-      <param name="in" value="TMTTenPlexMethod_test.mzML"/>
-      <output name="out" file="TMTElevenPlexMethod_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value="High-energy collision-induced dissociation"/>
-        <param name="reporter_mass_shift" value="0.002"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="type" value="tmt10plex"/>
-      <param name="in" value="MS3_nonHierarchical.mzML"/>
-      <output name="out" file="MS3TMT10Plex_test.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="extraction">
-        <param name="select_activation" value="Collision-induced dissociation"/>
-        <param name="reporter_mass_shift" value="0.002"/>
-        <param name="min_precursor_intensity" value="1.0"/>
-        <param name="keep_unannotated_precursor" value="true"/>
-        <param name="min_reporter_intensity" value="0.0"/>
-        <param name="discard_low_intensity_quantifications" value="false"/>
-        <param name="min_precursor_purity" value="0.0"/>
-        <param name="precursor_isotope_deviation" value="10.0"/>
-        <param name="purity_interpolation" value="true"/>
-      </section>
-      <section name="itraq4plex">
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="reference_channel" value="114"/>
-        <param name="correction_matrix" value="&quot;0.0/1.0/5.9/0.2&quot; &quot;0.0/2.0/5.6/0.1&quot; &quot;0.0/3.0/4.5/0.1&quot; &quot;0.1/4.0/3.5/0.1&quot;"/>
-      </section>
-      <section name="itraq8plex">
-        <param name="channel_113_description" value=""/>
-        <param name="channel_114_description" value=""/>
-        <param name="channel_115_description" value=""/>
-        <param name="channel_116_description" value=""/>
-        <param name="channel_117_description" value=""/>
-        <param name="channel_118_description" value=""/>
-        <param name="channel_119_description" value=""/>
-        <param name="channel_121_description" value=""/>
-        <param name="reference_channel" value="113"/>
-        <param name="correction_matrix" value="&quot;0.00/0.00/6.89/0.22&quot; &quot;0.00/0.94/5.90/0.16&quot; &quot;0.00/1.88/4.90/0.10&quot; &quot;0.00/2.82/3.90/0.07&quot; &quot;0.06/3.77/2.99/0.00&quot; &quot;0.09/4.71/1.88/0.00&quot; &quot;0.14/5.66/0.87/0.00&quot; &quot;0.27/7.44/0.18/0.00&quot;"/>
-      </section>
-      <section name="quantification">
-        <param name="isotope_correction" value="true"/>
-        <param name="normalization" value="false"/>
-      </section>
-      <section name="tmt10plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/5.09/0.0&quot; &quot;0.0/0.25/5.27/0.0&quot; &quot;0.0/0.37/5.36/0.15&quot; &quot;0.0/0.65/4.17/0.1&quot; &quot;0.08/0.49/3.06/0.0&quot; &quot;0.01/0.71/3.07/0.0&quot; &quot;0.0/1.32/2.62/0.0&quot; &quot;0.02/1.28/2.75/2.53&quot; &quot;0.03/2.08/2.23/0.0&quot; &quot;0.08/1.99/1.65/0.0&quot;"/>
-      </section>
-      <section name="tmt11plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <section name="tmt16plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127N_description" value=""/>
-        <param name="channel_127C_description" value=""/>
-        <param name="channel_128N_description" value=""/>
-        <param name="channel_128C_description" value=""/>
-        <param name="channel_129N_description" value=""/>
-        <param name="channel_129C_description" value=""/>
-        <param name="channel_130N_description" value=""/>
-        <param name="channel_130C_description" value=""/>
-        <param name="channel_131N_description" value=""/>
-        <param name="channel_131C_description" value=""/>
-        <param name="channel_132N_description" value=""/>
-        <param name="channel_132C_description" value=""/>
-        <param name="channel_133N_description" value=""/>
-        <param name="channel_133C_description" value=""/>
-        <param name="channel_134N_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/8.02/0.0&quot; &quot;0.0/0.68/7.46/0.0&quot; &quot;0.0/0.71/6.94/0.0&quot; &quot;0.0/1.88/6.67/0.0&quot; &quot;0.0/1.34/5.59/0.0&quot; &quot;0.0/2.41/5.48/0.0&quot; &quot;0.0/2.34/5.19/0.0&quot; &quot;0.0/3.53/4.57/0.0&quot; &quot;0.0/2.67/4.16/0.0&quot; &quot;0.0/3.92/3.73/0.0&quot; &quot;0.0/3.69/3.14/0.0&quot; &quot;0.0/3.22/2.76/0.0&quot; &quot;0.0/4.11/2.0/0.0&quot; &quot;0.0/3.85/1.58/0.0&quot; &quot;0.0/4.63/1.18/0.0&quot; &quot;0.0/5.22/0.86/0.0&quot;"/>
-      </section>
-      <section name="tmt6plex">
-        <param name="channel_126_description" value=""/>
-        <param name="channel_127_description" value=""/>
-        <param name="channel_128_description" value=""/>
-        <param name="channel_129_description" value=""/>
-        <param name="channel_130_description" value=""/>
-        <param name="channel_131_description" value=""/>
-        <param name="reference_channel" value="126"/>
-        <param name="correction_matrix" value="&quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot; &quot;0.0/0.0/0.0/0.0&quot;"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_LabeledEval">
-</xml>
-  <xml name="autotest_LuciphorAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="LuciphorAdapter_1_input.mzML"/>
-      <param name="id" value="LuciphorAdapter_1_input.idXML"/>
-      <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="fragment_method" value="CID"/>
-      <param name="fragment_mass_tolerance" value="0.5"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="min_mz" value="150.0"/>
-      <param name="target_modifications" value="Phospho (S),Phospho (T),Phospho (Y)"/>
-      <param name="neutral_losses" value="&quot;sty -H3PO4 -97.97690&quot;"/>
-      <param name="decoy_mass" value="79.966331"/>
-      <param name="decoy_neutral_losses" value="&quot;X -H3PO4 -97.97690&quot;"/>
-      <param name="max_charge_state" value="5"/>
-      <param name="max_peptide_length" value="40"/>
-      <param name="max_num_perm" value="16384"/>
-      <param name="modeling_score_threshold" value="0.95"/>
-      <param name="scoring_threshold" value="0.0"/>
-      <param name="min_num_psms_model" value="1"/>
-      <param name="run_mode" value="0"/>
-      <param name="rt_tolerance" value="0.01"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerIdentification">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
-      <output_collection name="out" count="1"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="1"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="2"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
-      <output_collection name="trafo_out" count="1"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.0"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="true"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerIdentification_7_input1.idXML"/>
-      <output_collection name="out" count="1"/>
-      <output_collection name="trafo_out" count="1"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="score_cutoff" value="false"/>
-        <param name="min_score" value="0.05"/>
-        <param name="min_run_occur" value="2"/>
-        <param name="max_rt_shift" value="0.5"/>
-        <param name="use_unassigned_peptides" value="true"/>
-        <param name="use_feature_rt" value="false"/>
-      </section>
-      <section name="model">
-        <param name="type" value="b_spline"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerPoseClustering">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
-      <output_collection name="out" count="3"/>
-      <output_collection name="trafo_out" count="3"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="true"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="30.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_2_input1.mzML,MapAlignerPoseClustering_2_input2.mzML,MapAlignerPoseClustering_2_input3.mzML"/>
-      <output_collection name="out" count="3"/>
-      <section name="reference">
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="false"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="100.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_1_input2.featureXML,MapAlignerPoseClustering_1_input3.featureXML"/>
-      <output_collection name="out" count="2"/>
-      <section name="reference">
-        <param name="file" value="MapAlignerPoseClustering_1_input1.featureXML"/>
-        <param name="index" value="0"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="true"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="30.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerPoseClustering_1_input1.featureXML,MapAlignerPoseClustering_1_input2.featureXML"/>
-      <output_collection name="trafo_out" count="2"/>
-      <section name="reference">
-        <param name="index" value="2"/>
-      </section>
-      <section name="algorithm">
-        <param name="max_num_peaks_considered" value="400"/>
-        <section name="superimposer">
-          <param name="mz_pair_max_distance" value="0.5"/>
-          <param name="rt_pair_distance_fraction" value="0.1"/>
-          <param name="num_used_points" value="2000"/>
-          <param name="scaling_bucket_size" value="0.005"/>
-          <param name="shift_bucket_size" value="3.0"/>
-          <param name="max_shift" value="1000.0"/>
-          <param name="max_scaling" value="2.0"/>
-          <param name="dump_buckets" value=""/>
-          <param name="dump_pairs" value=""/>
-        </section>
-        <section name="pairfinder">
-          <param name="second_nearest_gap" value="2.0"/>
-          <param name="use_identifications" value="false"/>
-          <param name="ignore_charge" value="true"/>
-          <param name="ignore_adduct" value="true"/>
-          <section name="distance_RT">
-            <param name="max_difference" value="30.0"/>
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_MZ">
-            <param name="max_difference" value="0.3"/>
-            <param name="unit" value="Da"/>
-            <param name="exponent" value="2.0"/>
-            <param name="weight" value="1.0"/>
-          </section>
-          <section name="distance_intensity">
-            <param name="exponent" value="1.0"/>
-            <param name="weight" value="0.0"/>
-            <param name="log_transform" value="disabled"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerSpectrum">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerSpectrum_1_input1.mzML,MapAlignerSpectrum_1_input2.mzML,MapAlignerSpectrum_1_input3.mzML"/>
-      <output_collection name="out" count="3"/>
-      <section name="algorithm">
-        <param name="gapcost" value="1.0"/>
-        <param name="affinegapcost" value="0.5"/>
-        <param name="cutoff_score" value="0.7"/>
-        <param name="bucketsize" value="100"/>
-        <param name="anchorpoints" value="100"/>
-        <param name="mismatchscore" value="-5.0"/>
-        <param name="scorefunction" value="SteinScottImproveScore"/>
-      </section>
-      <section name="model">
-        <param name="type" value="interpolated"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapAlignerTreeGuided">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
-      <output_collection name="out" count="3"/>
-      <section name="algorithm">
-        <param name="model_type" value="b_spline"/>
-        <section name="model">
-          <param name="type" value="b_spline"/>
-          <section name="linear">
-            <param name="symmetric_regression" value="false"/>
-            <param name="x_weight" value=""/>
-            <param name="y_weight" value=""/>
-            <param name="x_datum_min" value="1e-15"/>
-            <param name="x_datum_max" value="1000000000000000.0"/>
-            <param name="y_datum_min" value="1e-15"/>
-            <param name="y_datum_max" value="1000000000000000.0"/>
-          </section>
-          <section name="b_spline">
-            <param name="wavelength" value="0.0"/>
-            <param name="num_nodes" value="5"/>
-            <param name="extrapolate" value="linear"/>
-            <param name="boundary_condition" value="2"/>
-          </section>
-          <section name="lowess">
-            <param name="span" value="0.666666666666667"/>
-            <param name="num_iterations" value="3"/>
-            <param name="delta" value="-1.0"/>
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="four-point-linear"/>
-          </section>
-          <section name="interpolated">
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="two-point-linear"/>
-          </section>
-        </section>
-        <section name="align_algorithm">
-          <param name="score_cutoff" value="false"/>
-          <param name="min_score" value="0.05"/>
-          <param name="min_run_occur" value="2"/>
-          <param name="max_rt_shift" value="0.5"/>
-          <param name="use_unassigned_peptides" value="true"/>
-          <param name="use_feature_rt" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
-      <output_collection name="trafo_out" count="3"/>
-      <section name="algorithm">
-        <param name="model_type" value="b_spline"/>
-        <section name="model">
-          <param name="type" value="b_spline"/>
-          <section name="linear">
-            <param name="symmetric_regression" value="false"/>
-            <param name="x_weight" value=""/>
-            <param name="y_weight" value=""/>
-            <param name="x_datum_min" value="1e-15"/>
-            <param name="x_datum_max" value="1000000000000000.0"/>
-            <param name="y_datum_min" value="1e-15"/>
-            <param name="y_datum_max" value="1000000000000000.0"/>
-          </section>
-          <section name="b_spline">
-            <param name="wavelength" value="0.0"/>
-            <param name="num_nodes" value="5"/>
-            <param name="extrapolate" value="linear"/>
-            <param name="boundary_condition" value="2"/>
-          </section>
-          <section name="lowess">
-            <param name="span" value="0.666666666666667"/>
-            <param name="num_iterations" value="3"/>
-            <param name="delta" value="-1.0"/>
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="four-point-linear"/>
-          </section>
-          <section name="interpolated">
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="two-point-linear"/>
-          </section>
-        </section>
-        <section name="align_algorithm">
-          <param name="score_cutoff" value="false"/>
-          <param name="min_score" value="0.05"/>
-          <param name="min_run_occur" value="2"/>
-          <param name="max_rt_shift" value="0.5"/>
-          <param name="use_unassigned_peptides" value="true"/>
-          <param name="use_feature_rt" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapAlignerTreeGuided_1_input1.featureXML,MapAlignerTreeGuided_1_input2.featureXML,MapAlignerTreeGuided_1_input3.featureXML"/>
-      <output_collection name="out" count="3"/>
-      <section name="algorithm">
-        <param name="model_type" value="b_spline"/>
-        <section name="model">
-          <param name="type" value="b_spline"/>
-          <section name="linear">
-            <param name="symmetric_regression" value="false"/>
-            <param name="x_weight" value=""/>
-            <param name="y_weight" value=""/>
-            <param name="x_datum_min" value="1e-15"/>
-            <param name="x_datum_max" value="1000000000000000.0"/>
-            <param name="y_datum_min" value="1e-15"/>
-            <param name="y_datum_max" value="1000000000000000.0"/>
-          </section>
-          <section name="b_spline">
-            <param name="wavelength" value="0.0"/>
-            <param name="num_nodes" value="5"/>
-            <param name="extrapolate" value="linear"/>
-            <param name="boundary_condition" value="2"/>
-          </section>
-          <section name="lowess">
-            <param name="span" value="0.666666666666667"/>
-            <param name="num_iterations" value="3"/>
-            <param name="delta" value="-1.0"/>
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="four-point-linear"/>
-          </section>
-          <section name="interpolated">
-            <param name="interpolation_type" value="cspline"/>
-            <param name="extrapolation_type" value="two-point-linear"/>
-          </section>
-        </section>
-        <section name="align_algorithm">
-          <param name="score_cutoff" value="false"/>
-          <param name="min_score" value="0.05"/>
-          <param name="min_run_occur" value="2"/>
-          <param name="max_rt_shift" value="0.5"/>
-          <param name="use_unassigned_peptides" value="true"/>
-          <param name="use_feature_rt" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapNormalizer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_input.mzML"/>
-      <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapRTTransformer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_2_input.mzML"/>
-      <output name="out" file="MapRTTransformer_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="trafo_in" value="MapAlignerPoseClustering_1_trafo2.trafoXML"/>
-      <output name="trafo_out" file="MapRTTransformer_3_trafo.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="invert" value="true"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_4_input.chrom.mzML"/>
-      <output name="out" file="MapRTTransformer_4_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_none.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="false"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapRTTransformer_1_input.featureXML"/>
-      <output name="out" file="MapRTTransformer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo_in" value="MapRTTransformer_trafo_linear.trafoXML"/>
-      <param name="invert" value="false"/>
-      <param name="store_original_rt" value="true"/>
-      <section name="model">
-        <param name="type" value="none"/>
-        <section name="linear">
-          <param name="symmetric_regression" value="false"/>
-          <param name="x_weight" value=""/>
-          <param name="y_weight" value=""/>
-          <param name="x_datum_min" value="1e-15"/>
-          <param name="x_datum_max" value="1000000000000000.0"/>
-          <param name="y_datum_min" value="1e-15"/>
-          <param name="y_datum_max" value="1000000000000000.0"/>
-        </section>
-        <section name="b_spline">
-          <param name="wavelength" value="0.0"/>
-          <param name="num_nodes" value="5"/>
-          <param name="extrapolate" value="linear"/>
-          <param name="boundary_condition" value="2"/>
-        </section>
-        <section name="lowess">
-          <param name="span" value="0.666666666666667"/>
-          <param name="num_iterations" value="3"/>
-          <param name="delta" value="-1.0"/>
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="four-point-linear"/>
-        </section>
-        <section name="interpolated">
-          <param name="interpolation_type" value="cspline"/>
-          <param name="extrapolation_type" value="two-point-linear"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MapStatistics">
-</xml>
-  <xml name="autotest_MaRaClusterAdapter"/>
-  <xml name="autotest_MascotAdapterOnline">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="keep_protein_links" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="MascotAdapterOnline_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="Mascot_parameters">
-        <param name="database" value="SwissProt"/>
-        <param name="search_type" value="MIS"/>
-        <param name="enzyme" value="Trypsin"/>
-        <param name="instrument" value="Default"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="precursor_mass_tolerance" value="3.0"/>
-        <param name="precursor_error_units" value="Da"/>
-        <param name="fragment_mass_tolerance" value="0.3"/>
-        <param name="fragment_error_units" value="Da"/>
-        <param name="charges" value="1,2,3"/>
-        <param name="taxonomy" value="All entries"/>
-        <param name="fixed_modifications" value=""/>
-        <param name="variable_modifications" value=""/>
-        <param name="special_modifications" value="Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)"/>
-        <param name="mass_type" value="monoisotopic"/>
-        <param name="number_of_hits" value="0"/>
-        <param name="skip_spectrum_charges" value="false"/>
-        <param name="search_title" value="OpenMS_search"/>
-        <param name="username" value="OpenMS"/>
-        <param name="email" value="openmsjenkins@gmail.com"/>
-      </section>
-      <section name="Mascot_server">
-        <param name="hostname" value="www.matrixscience.com"/>
-        <param name="host_port" value="80"/>
-        <param name="server_path" value=""/>
-        <param name="timeout" value="1500"/>
-        <param name="boundary" value="GZWgAaYKjHFeUaLOLEIOMq"/>
-        <param name="use_proxy" value="false"/>
-        <param name="proxy_host" value=""/>
-        <param name="proxy_port" value="0"/>
-        <param name="proxy_username" value=""/>
-        <param name="proxy_password" value=""/>
-        <param name="login" value="false"/>
-        <param name="username" value=""/>
-        <param name="password" value=""/>
-        <param name="use_ssl" value="false"/>
-        <param name="export_params" value="_ignoreionsscorebelow=0&amp;_sigthreshold=0.99&amp;_showsubsets=1&amp;show_same_sets=1&amp;report=0&amp;percolate=0&amp;query_master=0"/>
-        <param name="skip_export" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MascotAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MascotAdapter_1_input.mzData"/>
-      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mgf"/>
-      <param name="instrument" value="ESI-TRAP"/>
-      <param name="precursor_mass_tolerance" value="1.3"/>
-      <param name="peak_mass_tolerance" value="0.3"/>
-      <param name="taxonomy" value=". . . . . . Chordata (vertebrates and relatives)"/>
-      <param name="modifications" value="&quot;Carboxymethyl (C)&quot;"/>
-      <param name="variable_modifications" value="&quot;Variable_Modifications_TEST_1&quot;"/>
-      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
-      <param name="db" value="MSDB"/>
-      <param name="hits" value="AUTO"/>
-      <param name="cleavage" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="sig_threshold" value="0.05"/>
-      <param name="pep_homol" value="1.0"/>
-      <param name="pep_ident" value="1.0"/>
-      <param name="pep_rank" value="1"/>
-      <param name="prot_score" value="1.0"/>
-      <param name="pep_score" value="1.0"/>
-      <param name="pep_exp_z" value="1"/>
-      <param name="show_unassigned" value="1"/>
-      <param name="first_dim_rt" value="0.0"/>
-      <param name="boundary" value="ABCDEFGHIJKMNOPQRSTUVWXYZ"/>
-      <param name="mass_type" value="Monoisotopic"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MascotAdapter_2_input.mascotXML"/>
-      <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="instrument" value="Default"/>
-      <param name="precursor_mass_tolerance" value="2.0"/>
-      <param name="peak_mass_tolerance" value="1.0"/>
-      <param name="taxonomy" value="All entries"/>
-      <param name="modifications" value=""/>
-      <param name="variable_modifications" value=""/>
-      <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
-      <param name="db" value="MSDB"/>
-      <param name="hits" value="AUTO"/>
-      <param name="cleavage" value="Trypsin"/>
-      <param name="missed_cleavages" value="0"/>
-      <param name="sig_threshold" value="0.05"/>
-      <param name="pep_homol" value="1.0"/>
-      <param name="pep_ident" value="1.0"/>
-      <param name="pep_rank" value="1"/>
-      <param name="prot_score" value="1.0"/>
-      <param name="pep_score" value="1.0"/>
-      <param name="pep_exp_z" value="1"/>
-      <param name="show_unassigned" value="1"/>
-      <param name="first_dim_rt" value="0.0"/>
-      <param name="boundary" value=""/>
-      <param name="mass_type" value="Monoisotopic"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MassCalculator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MassCalculator_1_input.tsv" ftype="tabular"/>
-      <param name="in_seq" value=""/>
-      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="charge" value="0 1"/>
-      <param name="format" value="table"/>
-      <param name="average_mass" value="false"/>
-      <param name="fragment_type" value="full"/>
-      <param name="separator" value=","/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
-      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="charge" value="1 2 3"/>
-      <param name="format" value="list"/>
-      <param name="average_mass" value="false"/>
-      <param name="fragment_type" value="full"/>
-      <param name="separator" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MassTraceExtractor">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MassTraceExtractor_1_input.mzML"/>
-      <output name="out" file="MassTraceExtractor_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="5.0"/>
-          <param name="max_trace_length" value="-1.0"/>
-        </section>
-        <section name="epd">
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-          <param name="enabled" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MassTraceExtractor_1_input.mzML"/>
-      <output name="out" file="MassTraceExtractor_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="out_type" value="featurexml"/>
-      <section name="algorithm">
-        <section name="common">
-          <param name="noise_threshold_int" value="10.0"/>
-          <param name="chrom_peak_snr" value="3.0"/>
-          <param name="chrom_fwhm" value="5.0"/>
-        </section>
-        <section name="mtd">
-          <param name="mass_error_ppm" value="20.0"/>
-          <param name="reestimate_mt_sd" value="true"/>
-          <param name="quant_method" value="area"/>
-          <param name="trace_termination_criterion" value="outlier"/>
-          <param name="trace_termination_outliers" value="5"/>
-          <param name="min_sample_rate" value="0.5"/>
-          <param name="min_trace_length" value="6.0"/>
-          <param name="max_trace_length" value="12.0"/>
-        </section>
-        <section name="epd">
-          <param name="width_filtering" value="off"/>
-          <param name="min_fwhm" value="3.0"/>
-          <param name="max_fwhm" value="60.0"/>
-          <param name="masstrace_snr_filtering" value="false"/>
-          <param name="enabled" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MetaboliteAdductDecharger">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
-      <output name="out_fm" file="MetaboliteAdductDecharger_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <section name="MetaboliteFeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="3"/>
-          <param name="charge_span_max" value="3"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.05"/>
-          <param name="unit" value="Da"/>
-          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
-          <param name="max_neutrals" value="1"/>
-          <param name="use_minority_bound" value="true"/>
-          <param name="max_minority_bound" value="3"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_fm_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MetaboliteAdductDecharger_input.featureXML"/>
-      <output name="out_cm" file="MetaboliteAdductDecharger_2_output_1.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="outpairs" file="MetaboliteAdductDecharger_2_output_2.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <section name="MetaboliteFeatureDeconvolution">
-          <param name="charge_min" value="1"/>
-          <param name="charge_max" value="3"/>
-          <param name="charge_span_max" value="3"/>
-          <param name="q_try" value="feature"/>
-          <param name="retention_max_diff" value="1.0"/>
-          <param name="retention_max_diff_local" value="1.0"/>
-          <param name="mass_max_diff" value="0.05"/>
-          <param name="unit" value="Da"/>
-          <param name="potential_adducts" value="&quot;H:+:0.4&quot; &quot;Na:+:0.25&quot; &quot;NH4:+:0.25&quot; &quot;K:+:0.1&quot; &quot;H-2O-1:0:0.05&quot;"/>
-          <param name="max_neutrals" value="1"/>
-          <param name="use_minority_bound" value="true"/>
-          <param name="max_minority_bound" value="3"/>
-          <param name="min_rt_overlap" value="0.66"/>
-          <param name="intensity_filter" value="false"/>
-          <param name="negative_mode" value="false"/>
-          <param name="default_map_label" value="decharged features"/>
-          <param name="verbose_level" value="0"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_cm_FLAG,outpairs_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MetaboliteSpectralMatcher">
-</xml>
-  <xml name="autotest_MetaProSIP">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_correlation_distance_to_averagine" value="-1.0"/>
-        <param name="pattern_15N_TIC_threshold" value="0.95"/>
-        <param name="pattern_13C_TIC_threshold" value="0.95"/>
-        <param name="pattern_2H_TIC_threshold" value="0.95"/>
-        <param name="pattern_18O_TIC_threshold" value="0.95"/>
-        <param name="heatmap_bins" value="20"/>
-        <param name="observed_peak_fraction" value="0.5"/>
-        <param name="min_consecutive_isotopes" value="2"/>
-        <param name="score_plot_yaxis_min" value="0.0"/>
-        <param name="collect_method" value="correlation_maximum"/>
-        <param name="lowRIA_correlation_threshold" value="-1.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
-      <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
-      <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
-      <param name="mz_tolerance_ppm" value="10.0"/>
-      <param name="rt_tolerance_s" value="30.0"/>
-      <param name="intensity_threshold" value="10.0"/>
-      <param name="correlation_threshold" value="0.7"/>
-      <param name="xic_threshold" value="0.7"/>
-      <param name="decomposition_threshold" value="0.7"/>
-      <param name="weight_merge_window" value="5.0"/>
-      <param name="plot_extension" value="png"/>
-      <param name="qc_output_directory" value=""/>
-      <param name="labeling_element" value="C"/>
-      <param name="use_unassigned_ids" value="false"/>
-      <param name="use_averagine_ids" value="false"/>
-      <param name="report_natural_peptides" value="false"/>
-      <param name="filter_monoisotopic" value="false"/>
-      <param name="cluster" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MRMMapper">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMMapping_input.chrom.mzML"/>
-      <param name="tr" value="MRMMapping_input.TraML"/>
-      <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="precursor_tolerance" value="0.3"/>
-        <param name="product_tolerance" value="0.3"/>
-        <param name="map_multiple_assays" value="false"/>
-        <param name="error_on_unmapped" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMMapping_input.chrom.mzML"/>
-      <param name="tr" value="MRMMapping_input_2.TraML"/>
-      <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="precursor_tolerance" value="0.01"/>
-        <param name="product_tolerance" value="0.01"/>
-        <param name="map_multiple_assays" value="false"/>
-        <param name="error_on_unmapped" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MRMPairFinder">
-</xml>
-  <xml name="autotest_MRMTransitionGroupPicker">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
-      <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
-      <output name="out" file="MRMTransitionGroupPicker_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="stop_after_feature" value="-1"/>
-        <param name="stop_after_intensity_ratio" value="0.0001"/>
-        <param name="min_peak_width" value="-1.0"/>
-        <param name="peak_integration" value="original"/>
-        <param name="background_subtraction" value="none"/>
-        <param name="recalculate_peaks" value="false"/>
-        <param name="use_precursors" value="false"/>
-        <param name="use_consensus" value="true"/>
-        <param name="recalculate_peaks_max_z" value="1.0"/>
-        <param name="minimal_quality" value="-10000.0"/>
-        <param name="resample_boundary" value="15.0"/>
-        <param name="compute_peak_quality" value="false"/>
-        <param name="compute_peak_shape_metrics" value="false"/>
-        <param name="compute_total_mi" value="false"/>
-        <param name="boundary_selection_method" value="largest"/>
-        <section name="PeakPickerMRM">
-          <param name="sgolay_frame_length" value="15"/>
-          <param name="sgolay_polynomial_order" value="3"/>
-          <param name="gauss_width" value="50.0"/>
-          <param name="use_gauss" value="true"/>
-          <param name="peak_width" value="40.0"/>
-          <param name="signal_to_noise" value="1.0"/>
-          <param name="sn_win_len" value="1000.0"/>
-          <param name="sn_bin_count" value="30"/>
-          <param name="write_sn_log_messages" value="false"/>
-          <param name="remove_overlapping_peaks" value="true"/>
-          <param name="method" value="legacy"/>
-        </section>
-        <section name="PeakIntegrator">
-          <param name="integration_type" value="intensity_sum"/>
-          <param name="baseline_type" value="base_to_base"/>
-          <param name="fit_EMG" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MRMTransitionGroupPicker_1_input.mzML"/>
-      <param name="tr" value="MRMTransitionGroupPicker_1_input.TraML"/>
-      <output name="out" file="MRMTransitionGroupPicker_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <section name="algorithm">
-        <param name="stop_after_feature" value="-1"/>
-        <param name="stop_after_intensity_ratio" value="0.0001"/>
-        <param name="min_peak_width" value="-1.0"/>
-        <param name="peak_integration" value="original"/>
-        <param name="background_subtraction" value="none"/>
-        <param name="recalculate_peaks" value="false"/>
-        <param name="use_precursors" value="false"/>
-        <param name="use_consensus" value="true"/>
-        <param name="recalculate_peaks_max_z" value="1.0"/>
-        <param name="minimal_quality" value="-10000.0"/>
-        <param name="resample_boundary" value="15.0"/>
-        <param name="compute_peak_quality" value="false"/>
-        <param name="compute_peak_shape_metrics" value="false"/>
-        <param name="compute_total_mi" value="true"/>
-        <param name="boundary_selection_method" value="largest"/>
-        <section name="PeakPickerMRM">
-          <param name="sgolay_frame_length" value="15"/>
-          <param name="sgolay_polynomial_order" value="3"/>
-          <param name="gauss_width" value="50.0"/>
-          <param name="use_gauss" value="true"/>
-          <param name="peak_width" value="40.0"/>
-          <param name="signal_to_noise" value="1.0"/>
-          <param name="sn_win_len" value="1000.0"/>
-          <param name="sn_bin_count" value="30"/>
-          <param name="write_sn_log_messages" value="false"/>
-          <param name="remove_overlapping_peaks" value="true"/>
-          <param name="method" value="legacy"/>
-        </section>
-        <section name="PeakIntegrator">
-          <param name="integration_type" value="intensity_sum"/>
-          <param name="baseline_type" value="base_to_base"/>
-          <param name="fit_EMG" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MSFraggerAdapter"/>
-  <xml name="autotest_MSGFPlusAdapter">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="add_decoys" value="false"/>
-        <param name="legacy_conversion" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="MSGFPlusAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="mzid_out" file="MSGFPlusAdapter_1_out2.tmp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="precursor_mass_tolerance" value="10.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="isotope_error_range" value="0,1"/>
-      <param name="fragment_method" value="from_spectrum"/>
-      <param name="instrument" value="high_res"/>
-      <param name="enzyme" value="Trypsin/P"/>
-      <param name="protocol" value="none"/>
-      <param name="tryptic" value="fully"/>
-      <param name="min_precursor_charge" value="1"/>
-      <param name="max_precursor_charge" value="3"/>
-      <param name="min_peptide_length" value="6"/>
-      <param name="max_peptide_length" value="40"/>
-      <param name="matches_per_spec" value="1"/>
-      <param name="add_features" value="false"/>
-      <param name="max_mods" value="2"/>
-      <param name="max_missed_cleavages" value="-1"/>
-      <param name="tasks" value="0"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mzid_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MSSimulator">
-</xml>
-  <xml name="autotest_MSstatsConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="retention_time_summarization_method" value="max"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSstatsConverter_1_in.consensusXML"/>
-      <param name="in_design" value="MSstatsConverter_1_design.tsv" ftype="tabular"/>
-      <param name="method" value="LFQ"/>
-      <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
-      <param name="msstats_condition" value="MSstats_Condition"/>
-      <param name="msstats_mixture" value="MSstats_Mixture"/>
-      <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_1_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="retention_time_summarization_method" value="manual"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSstatsConverter_2_in.consensusXML"/>
-      <param name="in_design" value="MSstatsConverter_2_design.tsv" ftype="tabular"/>
-      <param name="method" value="ISO"/>
-      <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
-      <param name="msstats_condition" value="MSstats_Condition"/>
-      <param name="msstats_mixture" value="MSstats_Mixture"/>
-      <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_2_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="retention_time_summarization_method" value="manual"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MSstatsConverter_3_in.consensusXML"/>
-      <param name="in_design" value="MSstatsConverter_3_design.tsv" ftype="tabular"/>
-      <param name="method" value="ISO"/>
-      <param name="msstats_bioreplicate" value="MSstats_BioReplicate"/>
-      <param name="msstats_condition" value="MSstats_Condition"/>
-      <param name="msstats_mixture" value="MSstats_Mixture"/>
-      <param name="labeled_reference_peptides" value="false"/>
-      <output name="out" file="MSstatsConverter_3_out.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MultiplexResolver">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="5"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
-        <param name="missed_cleavages" value="4"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="5"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
-      <output name="out" file="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[][Leu3]"/>
-        <param name="missed_cleavages" value="2"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="5"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
-      <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
-      <output name="out" file="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <output name="out_conflicts" file="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <section name="algorithm">
-        <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
-        <param name="missed_cleavages" value="3"/>
-        <param name="mass_tolerance" value="0.1"/>
-        <param name="mz_tolerance" value="10"/>
-        <param name="rt_tolerance" value="10"/>
-      </section>
-      <section name="labels">
-        <param name="Arg6" value="6.0201290268"/>
-        <param name="Arg10" value="10.0082686"/>
-        <param name="Lys4" value="4.0251069836"/>
-        <param name="Lys6" value="6.0201290268"/>
-        <param name="Lys8" value="8.0141988132"/>
-        <param name="Leu3" value="3.01883"/>
-        <param name="Dimethyl0" value="28.0313"/>
-        <param name="Dimethyl4" value="32.056407"/>
-        <param name="Dimethyl6" value="34.063117"/>
-        <param name="Dimethyl8" value="36.07567"/>
-        <param name="ICPL0" value="105.021464"/>
-        <param name="ICPL4" value="109.046571"/>
-        <param name="ICPL6" value="111.041593"/>
-        <param name="ICPL10" value="115.0667"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MyriMatchAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="MinPeptideMass" value="0.0"/>
-        <param name="MaxPeptideMass" value="10000.0"/>
-        <param name="MinPeptideLength" value="5"/>
-        <param name="MaxPeptideLength" value="75"/>
-        <param name="UseSmartPlusThreeModel" value="false"/>
-        <param name="NumIntensityClasses" value="3"/>
-        <param name="ClassSizeMultiplier" value="2.0"/>
-        <param name="MonoisotopeAdjustmentSet" value="[-1,2]"/>
-        <param name="SpectrumListFilters" value=""/>
-        <param name="ignoreConfigErrors" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="MyriMatchAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_mass_tolerance_unit" value="ppm"/>
-      <param name="precursor_mass_tolerance_avg" value="false"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="fragment_mass_tolerance_unit" value="Da"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="NumChargeStates" value="3"/>
-      <param name="TicCutoffPercentage" value="0.98"/>
-      <param name="MaxDynamicMods" value="2"/>
-      <param name="MaxResultRank" value="5"/>
-      <param name="CleavageRules" value=""/>
-      <param name="MinTerminiCleavages" value="2"/>
-      <param name="MaxMissedCleavages" value="-1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_MzMLSplitter"/>
-  <xml name="autotest_MzTabExporter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_1_input.consensusXML"/>
-      <output name="out" file="MzTabExporter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_2_input.idXML"/>
-      <output name="out" file="MzTabExporter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_3_input.featureXML"/>
-      <output name="out" file="MzTabExporter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="Epifany_2_out.consensusXML"/>
-      <output name="out" file="MzTabExporter_4_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_5_in.consensusXML"/>
-      <output name="out" file="MzTabExporter_5_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_6_input.idXML"/>
-      <output name="out" file="MzTabExporter_6_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="first_run_inference_only" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MzTabExporter_7_input.consensusXML"/>
-      <output name="out" file="MzTabExporter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="opt_columns" value="subfeatures"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_NoiseFilterGaussian">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="1.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="50.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_1_input.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="1.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterGaussian_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterGaussian_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="gaussian_width" value="50.0"/>
-        <param name="ppm_tolerance" value="10.0"/>
-        <param name="use_ppm_tolerance" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_NoiseFilterSGolay">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="9"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="11"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="9"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="frame_length" value="11"/>
-        <param name="polynomial_order" value="4"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_NovorAdapter"/>
-  <xml name="autotest_NucleicAcidSearchEngine">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="decharge_ms2" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
-      <param name="database" value="NucleicAcidSearchEngine_1.fasta"/>
-      <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="5.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="-2"/>
-        <param name="max_charge" value="-14"/>
-        <param name="include_unknown_charge" value="true"/>
-        <param name="use_avg_mass" value="false"/>
-        <param name="use_adducts" value="false"/>
-        <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
-        <param name="isotopes" value="0 1 2"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="5.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="ions" value="a-B,c,w,y"/>
-      </section>
-      <section name="modifications">
-        <param name="variable" value=""/>
-        <param name="variable_max_per_oligo" value="2"/>
-        <param name="resolve_ambiguities" value="false"/>
-      </section>
-      <section name="oligo">
-        <param name="min_size" value="5"/>
-        <param name="max_size" value="0"/>
-        <param name="missed_cleavages" value="22"/>
-        <param name="enzyme" value="no cleavage"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="1"/>
-      </section>
-      <section name="fdr">
-        <param name="decoy_pattern" value="DECOY_"/>
-        <param name="cutoff" value="0.05"/>
-        <param name="remove_decoys" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OMSSAAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="pc" value="1"/>
-        <param name="hs" value="4"/>
-        <param name="tez" value="1"/>
-        <param name="tom" value="0"/>
-        <param name="tem" value="0"/>
-        <param name="tex" value="1446.94"/>
-        <param name="zt" value="3"/>
-        <param name="z1" value="0.95"/>
-        <param name="zc" value="1"/>
-        <param name="zcc" value="2"/>
-        <param name="zoh" value="2"/>
-        <param name="no" value="4"/>
-        <param name="nox" value="40"/>
-        <param name="i" value="1,4"/>
-        <param name="sp" value="100"/>
-        <param name="sb1" value="1"/>
-        <param name="sct" value="0"/>
-        <param name="x" value="0"/>
-        <param name="hm" value="2"/>
-        <param name="ht" value="6"/>
-        <param name="mm" value="128"/>
-        <param name="mnm" value="false"/>
-        <param name="is" value="0.0"/>
-        <param name="ir" value="0.0"/>
-        <param name="ii" value="0.0"/>
-        <param name="chunk_size" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="OMSSAAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="min_precursor_charge" value="1"/>
-      <param name="max_precursor_charge" value="3"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="v" value="1"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="hl" value="30"/>
-      <param name="he" value="1.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenPepXLLF">
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenPepXLLF_input.mzML"/>
-      <param name="database" value="OpenPepXLLF_input.fasta"/>
-      <param name="decoy_string" value="decoy"/>
-      <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXLLF_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="OpenPepXLLF_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquestxml" file="OpenPepXLLF_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <output name="out_xquest_specxml" file="OpenPepXLLF_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="3"/>
-        <param name="max_charge" value="7"/>
-        <param name="corrections" value="2 1 0"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_xlinks" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="5"/>
-        <param name="missed_cleavages" value="2"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="cross_linker">
-        <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="mass" value="138.0680796"/>
-        <param name="mass_mono_link" value="156.07864431 155.094628715"/>
-        <param name="name" value="DSS"/>
-      </section>
-      <section name="algorithm">
-        <param name="number_top_hits" value="5"/>
-        <param name="deisotope" value="auto"/>
-        <param name="use_sequence_tags" value="false"/>
-        <param name="sequence_tag_min_length" value="2"/>
-      </section>
-      <section name="ions">
-        <param name="b_ions" value="true"/>
-        <param name="y_ions" value="true"/>
-        <param name="a_ions" value="false"/>
-        <param name="x_ions" value="false"/>
-        <param name="c_ions" value="false"/>
-        <param name="z_ions" value="false"/>
-        <param name="neutral_losses" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenPepXLLF_input2.mzML"/>
-      <param name="database" value="OpenPepXLLF_input2.fasta"/>
-      <param name="decoy_string" value="decoy_"/>
-      <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXLLF_output2.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="3"/>
-        <param name="max_charge" value="7"/>
-        <param name="corrections" value="1 0"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="0.2"/>
-        <param name="mass_tolerance_xlinks" value="0.3"/>
-        <param name="mass_tolerance_unit" value="Da"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value="Carbamidomethyl (C)"/>
-        <param name="variable" value="Oxidation (M)"/>
-        <param name="variable_max_per_peptide" value="1"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="5"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="cross_linker">
-        <param name="residue1" value="&quot;D&quot; &quot;E&quot; &quot;C-term&quot;"/>
-        <param name="residue2" value="&quot;K&quot; &quot;S&quot; &quot;T&quot; &quot;Y&quot; &quot;N-term&quot;"/>
-        <param name="mass" value="-18.010595"/>
-        <param name="mass_mono_link" value=""/>
-        <param name="name" value="DMTMM"/>
-      </section>
-      <section name="algorithm">
-        <param name="number_top_hits" value="1"/>
-        <param name="deisotope" value="auto"/>
-        <param name="use_sequence_tags" value="false"/>
-        <param name="sequence_tag_min_length" value="2"/>
-      </section>
-      <section name="ions">
-        <param name="b_ions" value="true"/>
-        <param name="y_ions" value="true"/>
-        <param name="a_ions" value="false"/>
-        <param name="x_ions" value="false"/>
-        <param name="c_ions" value="false"/>
-        <param name="z_ions" value="false"/>
-        <param name="neutral_losses" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenPepXL">
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenPepXL_input.mzML"/>
-      <param name="consensus" value="OpenPepXL_input.consensusXML"/>
-      <param name="database" value="OpenPepXL_input.fasta"/>
-      <param name="decoy_string" value="decoy"/>
-      <param name="decoy_prefix" value="true"/>
-      <output name="out_idXML" file="OpenPepXL_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="OpenPepXL_output.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquestxml" file="OpenPepXL_output.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <output name="out_xquest_specxml" file="OpenPepXL_output.spec.xml" compare="sim_size" delta="5700" ftype="spec.xml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="3"/>
-        <param name="max_charge" value="7"/>
-        <param name="corrections" value="2 1 0"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="0.2"/>
-        <param name="mass_tolerance_xlinks" value="0.3"/>
-        <param name="mass_tolerance_unit" value="Da"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="5"/>
-        <param name="missed_cleavages" value="2"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="cross_linker">
-        <param name="residue1" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="residue2" value="&quot;K&quot; &quot;N-term&quot;"/>
-        <param name="mass_light" value="138.0680796"/>
-        <param name="mass_iso_shift" value="12.075321"/>
-        <param name="mass_mono_link" value="156.07864431 155.094628715"/>
-        <param name="name" value="DSS"/>
-      </section>
-      <section name="algorithm">
-        <param name="number_top_hits" value="5"/>
-        <param name="deisotope" value="auto"/>
-      </section>
-      <section name="ions">
-        <param name="b_ions" value="true"/>
-        <param name="y_ions" value="true"/>
-        <param name="a_ions" value="false"/>
-        <param name="x_ions" value="false"/>
-        <param name="c_ions" value="false"/>
-        <param name="z_ions" value="false"/>
-        <param name="neutral_losses" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquestxml_FLAG,out_xquest_specxml_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathAnalyzer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_mod_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_5_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="true"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="8.0"/>
-          <param name="dia_byseries_ppm_diff" value="15.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_6_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="true"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="8.0"/>
-          <param name="dia_byseries_ppm_diff" value="15.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <output name="out" file="OpenSwathAnalyzer_7_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="original"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="true"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_8_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_9_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_10_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <param name="tr" value="OpenSwathAnalyzer_1_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathAnalyzer_input.trafoXML"/>
-      <output name="out" file="OpenSwathAnalyzer_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="no_strict" value="false"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="40.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="legacy"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathAssayGenerator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_num_alternative_localizations" value="10000"/>
-        <param name="disable_identification_ms2_precursors" value="false"/>
-        <param name="disable_identification_specific_losses" value="false"/>
-        <param name="enable_identification_unspecific_losses" value="false"/>
-        <param name="enable_swath_specifity" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="min_transitions" value="6"/>
-      <param name="max_transitions" value="6"/>
-      <param name="allowed_fragment_types" value="b,y"/>
-      <param name="allowed_fragment_charges" value="2,3"/>
-      <param name="enable_detection_specific_losses" value="true"/>
-      <param name="enable_detection_unspecific_losses" value="false"/>
-      <param name="precursor_mz_threshold" value="0.025"/>
-      <param name="precursor_lower_mz_limit" value="400.0"/>
-      <param name="precursor_upper_mz_limit" value="1200.0"/>
-      <param name="product_mz_threshold" value="0.025"/>
-      <param name="product_lower_mz_limit" value="350.0"/>
-      <param name="product_upper_mz_limit" value="2000.0"/>
-      <param name="enable_ipf" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_num_alternative_localizations" value="10000"/>
-        <param name="disable_identification_ms2_precursors" value="false"/>
-        <param name="disable_identification_specific_losses" value="false"/>
-        <param name="enable_identification_unspecific_losses" value="false"/>
-        <param name="enable_swath_specifity" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="min_transitions" value="6"/>
-      <param name="max_transitions" value="6"/>
-      <param name="allowed_fragment_types" value="b,y"/>
-      <param name="allowed_fragment_charges" value="1,2,3,4"/>
-      <param name="enable_detection_specific_losses" value="false"/>
-      <param name="enable_detection_unspecific_losses" value="false"/>
-      <param name="precursor_mz_threshold" value="0.025"/>
-      <param name="precursor_lower_mz_limit" value="400.0"/>
-      <param name="precursor_upper_mz_limit" value="1200.0"/>
-      <param name="product_mz_threshold" value="0.025"/>
-      <param name="product_lower_mz_limit" value="350.0"/>
-      <param name="product_upper_mz_limit" value="2000.0"/>
-      <param name="unimod_file" value="OpenSwathAssayGenerator_input_2_unimod.xml"/>
-      <param name="enable_ipf" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_num_alternative_localizations" value="10000"/>
-        <param name="disable_identification_ms2_precursors" value="false"/>
-        <param name="disable_identification_specific_losses" value="false"/>
-        <param name="enable_identification_unspecific_losses" value="false"/>
-        <param name="enable_swath_specifity" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="min_transitions" value="6"/>
-      <param name="max_transitions" value="6"/>
-      <param name="allowed_fragment_types" value="b,y"/>
-      <param name="allowed_fragment_charges" value="1,2,3,4"/>
-      <param name="enable_detection_specific_losses" value="false"/>
-      <param name="enable_detection_unspecific_losses" value="false"/>
-      <param name="precursor_mz_threshold" value="0.025"/>
-      <param name="precursor_lower_mz_limit" value="400.0"/>
-      <param name="precursor_upper_mz_limit" value="1200.0"/>
-      <param name="product_mz_threshold" value="0.025"/>
-      <param name="product_lower_mz_limit" value="350.0"/>
-      <param name="product_upper_mz_limit" value="2000.0"/>
-      <param name="unimod_file" value="OpenSwathAssayGenerator_input_3_unimod.xml"/>
-      <param name="enable_ipf" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathChromatogramExtractor">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="false"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="50.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="false"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="true"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="true"/>
-      <param name="extract_MS1" value="false"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
-      <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="min_upper_edge_dist" value="0.0"/>
-      <param name="rt_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_window" value="0.05"/>
-      <param name="ppm" value="false"/>
-      <param name="is_swath" value="false"/>
-      <param name="extract_MS1" value="true"/>
-      <section name="model">
-        <param name="type" value="linear"/>
-        <param name="symmetric_regression" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathConfidenceScoring">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="lib" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathConfidenceScoring_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="trafo" value="OpenSwathConfidenceScoring_1_input.trafoXML"/>
-      <param name="decoys" value="1"/>
-      <param name="transitions" value="2"/>
-      <section name="GLM">
-        <param name="intercept" value="3.87333466"/>
-        <param name="delta_rt" value="-0.02898629"/>
-        <param name="dist_int" value="-7.75880768"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathDecoyGenerator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.8"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.025"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="false"/>
-        <param name="enable_detection_unspecific_losses" value="false"/>
-        <param name="separate" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.8"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.8"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="false"/>
-        <param name="enable_detection_unspecific_losses" value="false"/>
-        <param name="separate" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input_2.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_2.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.8"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.025"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="false"/>
-        <param name="enable_detection_unspecific_losses" value="false"/>
-        <param name="separate" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input_3.TraML"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_3.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="min_decoy_fraction" value="0.4"/>
-        <param name="aim_decoy_fraction" value="1.0"/>
-        <param name="shuffle_max_attempts" value="30"/>
-        <param name="shuffle_sequence_identity_threshold" value="0.5"/>
-        <param name="shift_precursor_mz_shift" value="0.0"/>
-        <param name="shift_product_mz_shift" value="20.0"/>
-        <param name="product_mz_threshold" value="0.025"/>
-        <param name="allowed_fragment_types" value="b,y"/>
-        <param name="allowed_fragment_charges" value="1,2,3,4"/>
-        <param name="enable_detection_specific_losses" value="true"/>
-        <param name="enable_detection_unspecific_losses" value="true"/>
-        <param name="separate" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathDecoyGenerator_input_4.tsv" ftype="tabular"/>
-      <output name="out" file="OpenSwathDecoyGenerator_output_4.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <param name="method" value="pseudo-reverse"/>
-      <param name="decoy_tag" value="DECOY_"/>
-      <param name="switchKR" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathDIAPreScoring">
-</xml>
-  <xml name="autotest_OpenSwathFeatureXMLToTSV">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="short_format" value="true"/>
-      <param name="best_scoring_peptide" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="short_format" value="false"/>
-      <param name="best_scoring_peptide" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-      <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="short_format" value="true"/>
-      <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathFileSplitter"/>
-  <xml name="autotest_OpenSwathMzMLFileCacher">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_2_input.chrom.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="0.0001"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
-      <param name="out_type" value="sqmass"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_3_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_3_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_2_input.chrom.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_input.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
-      <param name="out_type" value="sqmass"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_4_input.tmp.sqMass"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_4_output.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="true"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathMzMLFileCacher_1_input.mzML"/>
-      <output name="out" file="OpenSwathMzMLFileCacher_1_input.cached.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_swathfile.mzML.cached.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="-1.0"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathAnalyzer_1_input_chrom.mzML"/>
-      <output name="out" file="OpenSwathAnalyzer_4_input_chrom.mzML.cached.tmp" compare="sim_size" delta="5700"/>
-      <param name="out_type" value="mzML"/>
-      <param name="lossy_compression" value="true"/>
-      <param name="full_meta" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="lossy_mass_accuracy" value="0.0001"/>
-        <param name="process_lowmemory" value="false"/>
-        <param name="lowmem_batchsize" value="500"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_14.chrom.tmp.sqMass"/>
-      <output name="out" file="OpenSwathWorkflow_14.chrom.tmp.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="out_type" value="mzml"/>
-      <param name="lossy_compression" value="false"/>
-      <param name="full_meta" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathRewriteToFeatureXML">
-</xml>
-  <xml name="autotest_OpenSwathRTNormalizer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
-      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_1_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="min_rsq" value="0.95"/>
-      <param name="min_coverage" value="0.6"/>
-      <param name="estimateBestPeptides" value="false"/>
-      <section name="RTNormalization">
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <section name="peptideEstimation">
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
-      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_3_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="min_rsq" value="0.95"/>
-      <param name="min_coverage" value="0.6"/>
-      <param name="estimateBestPeptides" value="true"/>
-      <section name="RTNormalization">
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <section name="peptideEstimation">
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="3"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="3"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathRTNormalizer_1_input.mzML"/>
-      <param name="tr" value="OpenSwathRTNormalizer_1_input.TraML"/>
-      <output name="out" file="OpenSwathRTNormalizer_4_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <param name="min_rsq" value="0.95"/>
-      <param name="min_coverage" value="0.6"/>
-      <param name="estimateBestPeptides" value="false"/>
-      <section name="RTNormalization">
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-      </section>
-      <section name="algorithm">
-        <param name="stop_report_after_feature" value="-1"/>
-        <param name="rt_extraction_window" value="-1.0"/>
-        <param name="rt_normalization_factor" value="1.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="stop_after_intensity_ratio" value="0.0001"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="false"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="1.0"/>
-          <param name="minimal_quality" value="-10000.0"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="15"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="50.0"/>
-            <param name="use_gauss" value="true"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="1.0"/>
-            <param name="sn_win_len" value="1000.0"/>
-            <param name="sn_bin_count" value="30"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="false"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="interpolation_step" value="0.2"/>
-          <param name="tolerance_stdev_bounding_box" value="3.0"/>
-          <param name="max_iteration" value="500"/>
-          <section name="statistics">
-            <param name="mean" value="1.0"/>
-            <param name="variance" value="1.0"/>
-          </section>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_elution_model_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <section name="peptideEstimation">
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_OpenSwathWorkflow">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="false"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_1_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <output name="out_qc" file="OpenSwathWorkflow_1_output.json" compare="sim_size" delta="5700" ftype="json"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,out_qc_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_2_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="false"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_2_input.mzXML"/>
-      <param name="tr" value="OpenSwathWorkflow_2_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_2_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_tsv" file="OpenSwathWorkflow_4.tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_4.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="cache"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="cacheWorkingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <param name="swath_windows_file" value="swath_windows.txt" ftype="txt"/>
-      <output name="out_features" file="OpenSwathWorkflow_3_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_3_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="true"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <param name="swath_windows_file" value="swath_windows_overlap.txt" ftype="txt"/>
-      <output name="out_features" file="OpenSwathWorkflow_10.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_10.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="false"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="550.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="quadratic_regression_delta_ppm"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_11_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_11_input_2.TraML"/>
-      <param name="tr_type" value=""/>
-      <param name="tr_irt" value="OpenSwathWorkflow_11_input.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_11_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_11_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="true"/>
-      <param name="rt_extraction_window" value="-1.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.2"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="none"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="true"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_13_input.pqp.tmp"/>
-      <param name="tr_type" value="pqp"/>
-      <output name="out_osw" file="OpenSwathWorkflow_13.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_13_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="sqMass"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_14_input.pqp.tmp"/>
-      <param name="tr_type" value="pqp"/>
-      <output name="out_osw" file="OpenSwathWorkflow_14.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_14.chrom.tmp.sqMass" compare="sim_size" delta="5700" ftype="sqmass"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_osw_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="2"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_15_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_15_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_15_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="true"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="2"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_16_input.sqMass"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_16_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_16_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="true"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="cache"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_17.featureXML.tmp" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17.chrom.mzML.tmp" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="true"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="false"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_17_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_17_input.pqp.tmp"/>
-      <param name="tr_type" value="pqp"/>
-      <output name="out_features" file="OpenSwathWorkflow_17_b_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_17_b_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="0.05"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_18_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="false"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_19_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="rt_norm" value="OpenSwathWorkflow_1_input.trafoXML"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_20_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="Th"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="false"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="normal"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_21_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_21_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <param name="tr_irt" value="OpenSwathWorkflow_21_input.irt.TraML"/>
-      <output name="out_features" file="OpenSwathWorkflow_21_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_21_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="0.05"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <output name="Debugging_irt_trafo" file="OpenSwathWorkflow_21_output.trafoXML" compare="sim_size" delta="5700" ftype="trafoxml"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.6666666666666666"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="true"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="true"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="false"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG,irt_trafo_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="sort_swath_maps" value="false"/>
-        <param name="enable_ms1" value="true"/>
-        <param name="enable_ipf" value="true"/>
-        <param name="out_chrom_type" value="mzML"/>
-        <param name="min_upper_edge_dist" value="0.0"/>
-        <param name="extra_rt_extraction_window" value="0.0"/>
-        <param name="mz_extraction_window_unit" value="ppm"/>
-        <param name="mz_extraction_window_ms1_unit" value="ppm"/>
-        <param name="use_ms1_ion_mobility" value="true"/>
-        <param name="matching_window_only" value="true"/>
-        <param name="irt_mz_extraction_window" value="50.0"/>
-        <param name="irt_mz_extraction_window_unit" value="ppm"/>
-        <param name="irt_im_extraction_window" value="-1.0"/>
-        <param name="min_rsq" value="0.95"/>
-        <param name="min_coverage" value="0.6"/>
-        <param name="split_file_input" value="false"/>
-        <param name="use_elution_model_score" value="false"/>
-        <param name="readOptions" value="workingInMemory"/>
-        <param name="mz_correction_function" value="none"/>
-        <param name="extraction_function" value="tophat"/>
-        <param name="batchSize" value="1000"/>
-        <param name="ms1_isotopes" value="3"/>
-        <param name="force" value="false"/>
-        <param name="test" value="false"/>
-      </conditional>
-      <param name="in" value="OpenSwathWorkflow_22_input.mzML"/>
-      <param name="tr" value="OpenSwathWorkflow_22_input.tsv" ftype="tabular"/>
-      <param name="tr_type" value=""/>
-      <output name="out_features" file="OpenSwathWorkflow_22_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <output name="out_chrom" file="OpenSwathWorkflow_22_output.chrom.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="sonar" value="false"/>
-      <param name="rt_extraction_window" value="600.0"/>
-      <param name="ion_mobility_window" value="-1.0"/>
-      <param name="mz_extraction_window" value="50.0"/>
-      <param name="mz_extraction_window_ms1" value="50.0"/>
-      <param name="im_extraction_window_ms1" value="-1.0"/>
-      <section name="Debugging"/>
-      <section name="Calibration">
-        <param name="ms1_im_calibration" value="false"/>
-        <param name="im_correction_function" value="linear"/>
-        <param name="debug_im_file" value=""/>
-        <param name="debug_mz_file" value=""/>
-      </section>
-      <section name="Library">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <section name="RTNormalization">
-        <param name="alignmentMethod" value="linear"/>
-        <param name="outlierMethod" value="iter_residual"/>
-        <param name="useIterativeChauvenet" value="false"/>
-        <param name="RANSACMaxIterations" value="1000"/>
-        <param name="RANSACMaxPercentRTThreshold" value="3"/>
-        <param name="RANSACSamplingSize" value="10"/>
-        <param name="estimateBestPeptides" value="false"/>
-        <param name="InitialQualityCutoff" value="0.5"/>
-        <param name="OverallQualityCutoff" value="5.5"/>
-        <param name="NrRTBins" value="10"/>
-        <param name="MinPeptidesPerBin" value="1"/>
-        <param name="MinBinsFilled" value="8"/>
-        <section name="lowess">
-          <param name="span" value="0.05"/>
-        </section>
-        <section name="b_spline">
-          <param name="num_nodes" value="5"/>
-        </section>
-      </section>
-      <section name="Scoring">
-        <param name="stop_report_after_feature" value="5"/>
-        <param name="rt_normalization_factor" value="100.0"/>
-        <param name="quantification_cutoff" value="0.0"/>
-        <param name="write_convex_hull" value="false"/>
-        <param name="spectrum_addition_method" value="simple"/>
-        <param name="add_up_spectra" value="1"/>
-        <param name="spacing_for_spectra_resampling" value="0.005"/>
-        <param name="uis_threshold_sn" value="-1"/>
-        <param name="uis_threshold_peak_area" value="0"/>
-        <param name="scoring_model" value="default"/>
-        <param name="im_extra_drift" value="0.0"/>
-        <param name="strict" value="true"/>
-        <section name="TransitionGroupPicker">
-          <param name="stop_after_feature" value="-1"/>
-          <param name="min_peak_width" value="-1.0"/>
-          <param name="peak_integration" value="original"/>
-          <param name="background_subtraction" value="none"/>
-          <param name="recalculate_peaks" value="true"/>
-          <param name="use_precursors" value="false"/>
-          <param name="use_consensus" value="true"/>
-          <param name="recalculate_peaks_max_z" value="0.75"/>
-          <param name="minimal_quality" value="-1.5"/>
-          <param name="resample_boundary" value="15.0"/>
-          <param name="compute_peak_quality" value="false"/>
-          <param name="compute_peak_shape_metrics" value="false"/>
-          <param name="compute_total_mi" value="false"/>
-          <param name="boundary_selection_method" value="largest"/>
-          <section name="PeakPickerMRM">
-            <param name="sgolay_frame_length" value="11"/>
-            <param name="sgolay_polynomial_order" value="3"/>
-            <param name="gauss_width" value="30.0"/>
-            <param name="use_gauss" value="false"/>
-            <param name="peak_width" value="-1.0"/>
-            <param name="signal_to_noise" value="0.1"/>
-            <param name="write_sn_log_messages" value="false"/>
-            <param name="remove_overlapping_peaks" value="true"/>
-            <param name="method" value="corrected"/>
-          </section>
-          <section name="PeakIntegrator">
-            <param name="integration_type" value="intensity_sum"/>
-            <param name="baseline_type" value="base_to_base"/>
-            <param name="fit_EMG" value="false"/>
-          </section>
-        </section>
-        <section name="DIAScoring">
-          <param name="dia_extraction_window" value="0.05"/>
-          <param name="dia_extraction_unit" value="Th"/>
-          <param name="dia_centroided" value="false"/>
-          <param name="dia_byseries_intensity_min" value="300.0"/>
-          <param name="dia_byseries_ppm_diff" value="10.0"/>
-          <param name="dia_nr_isotopes" value="4"/>
-          <param name="dia_nr_charges" value="4"/>
-          <param name="peak_before_mono_max_ppm_diff" value="20.0"/>
-        </section>
-        <section name="EMGScoring">
-          <param name="max_iteration" value="10"/>
-        </section>
-        <section name="Scores">
-          <param name="use_shape_score" value="true"/>
-          <param name="use_coelution_score" value="true"/>
-          <param name="use_rt_score" value="true"/>
-          <param name="use_library_score" value="true"/>
-          <param name="use_intensity_score" value="true"/>
-          <param name="use_nr_peaks_score" value="true"/>
-          <param name="use_total_xic_score" value="true"/>
-          <param name="use_total_mi_score" value="false"/>
-          <param name="use_sn_score" value="true"/>
-          <param name="use_mi_score" value="true"/>
-          <param name="use_dia_scores" value="true"/>
-          <param name="use_ms1_correlation" value="false"/>
-          <param name="use_sonar_scores" value="false"/>
-          <param name="use_ion_mobility_scores" value="false"/>
-          <param name="use_ms1_fullscan" value="false"/>
-          <param name="use_ms1_mi" value="true"/>
-          <param name="use_uis_scores" value="false"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_features_FLAG,out_chrom_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PeakPickerHiRes">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_output_lowMem.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="lowmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_2_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="1.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value="1"/>
-        <param name="report_FWHM" value="true"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="processOption" value="inmemory"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerHiRes_5_input.mzML"/>
-      <output name="out" file="PeakPickerHiRes_5_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="0.0"/>
-        <param name="spacing_difference_gap" value="4.0"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="missing" value="1"/>
-        <param name="ms_levels" value=""/>
-        <param name="report_FWHM" value="false"/>
-        <param name="report_FWHM_unit" value="relative"/>
-        <section name="SignalToNoise">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-          <param name="write_log_messages" value="true"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PeakPickerIterative">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerIterative_1_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise_" value="1.0"/>
-        <param name="peak_width" value="0.04"/>
-        <param name="spacing_difference" value="1.5"/>
-        <param name="sn_bin_count_" value="30"/>
-        <param name="nr_iterations_" value="5"/>
-        <param name="sn_win_len_" value="20.0"/>
-        <param name="check_width_internally" value="false"/>
-        <param name="ms1_only" value="false"/>
-        <param name="clear_meta_data" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerIterative_2_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise_" value="0.0"/>
-        <param name="peak_width" value="0.04"/>
-        <param name="spacing_difference" value="2.5"/>
-        <param name="sn_bin_count_" value="30"/>
-        <param name="nr_iterations_" value="5"/>
-        <param name="sn_win_len_" value="20.0"/>
-        <param name="check_width_internally" value="true"/>
-        <param name="ms1_only" value="false"/>
-        <param name="clear_meta_data" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PeakPickerWavelet">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="3.0"/>
-        <param name="centroid_percentage" value="0.6"/>
-        <param name="peak_width" value="0.2"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="0.5"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="100.0"/>
-          <param name="peak_bound_ms2_level" value="10.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="false"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.12"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="10"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_deconv_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_deconv_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="2.0"/>
-        <param name="centroid_percentage" value="0.8"/>
-        <param name="peak_width" value="0.15"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="1.0"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="200.0"/>
-          <param name="peak_bound_ms2_level" value="50.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="true"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.1"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="100"/>
-            <section name="penalties">
-              <param name="position" value="1.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="3.0"/>
-        <param name="centroid_percentage" value="0.6"/>
-        <param name="peak_width" value="0.2"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="0.5"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="100.0"/>
-          <param name="peak_bound_ms2_level" value="10.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="false"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.12"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="10"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="write_peak_meta_data" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeakPickerWavelet_input.mzML"/>
-      <output name="out" file="PeakPickerWavelet_output_noMetaData.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="signal_to_noise" value="3.0"/>
-        <param name="centroid_percentage" value="0.6"/>
-        <param name="peak_width" value="0.2"/>
-        <param name="estimate_peak_width" value="false"/>
-        <param name="fwhm_lower_bound_factor" value="0.5"/>
-        <param name="fwhm_upper_bound_factor" value="20.0"/>
-        <section name="optimization">
-          <param name="iterations" value="400"/>
-          <section name="penalties">
-            <param name="position" value="0.0"/>
-            <param name="left_width" value="1.0"/>
-            <param name="right_width" value="1.0"/>
-            <param name="height" value="1.0"/>
-          </section>
-          <section name="2d">
-            <param name="tolerance_mz" value="2.2"/>
-            <param name="max_peak_distance" value="1.2"/>
-          </section>
-        </section>
-        <section name="thresholds">
-          <param name="peak_bound" value="100.0"/>
-          <param name="peak_bound_ms2_level" value="10.0"/>
-          <param name="correlation" value="0.5"/>
-          <param name="noise_level" value="0.1"/>
-          <param name="search_radius" value="3"/>
-        </section>
-        <section name="wavelet_transform">
-          <param name="spacing" value="0.001"/>
-        </section>
-        <section name="deconvolution">
-          <param name="deconvolution" value="false"/>
-          <param name="asym_threshold" value="0.3"/>
-          <param name="left_width" value="2.0"/>
-          <param name="right_width" value="2.0"/>
-          <param name="scaling" value="0.12"/>
-          <section name="fitting">
-            <param name="fwhm_threshold" value="0.7"/>
-            <param name="eps_abs" value="9.999999747378752e-06"/>
-            <param name="eps_rel" value="9.999999747378752e-06"/>
-            <param name="max_iteration" value="10"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="height" value="1.0"/>
-              <param name="left_width" value="0.0"/>
-              <param name="right_width" value="0.0"/>
-            </section>
-          </section>
-        </section>
-        <section name="SignalToNoiseEstimationParameter">
-          <param name="max_intensity" value="-1"/>
-          <param name="auto_max_stdev_factor" value="3.0"/>
-          <param name="auto_max_percentile" value="95"/>
-          <param name="auto_mode" value="0"/>
-          <param name="win_len" value="200.0"/>
-          <param name="bin_count" value="30"/>
-          <param name="stdev_mp" value="3.0"/>
-          <param name="min_required_elements" value="10"/>
-          <param name="noise_for_empty_window" value="1e+20"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PepNovoAdapter">
-</xml>
-  <xml name="autotest_PeptideIndexer">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="true"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="0"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_2.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="3"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_3.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="full"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_3.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="semi"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_3.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="remove"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_10_input.idXML"/>
-      <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
-      <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="error"/>
-      <param name="aaa_max" value="3"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="true"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="auto"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_1.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="warn"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="empty.idXML"/>
-      <param name="fasta" value="PeptideIndexer_1.fasta"/>
-      <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="false"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="error"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="auto"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PeptideIndexer_14.idXML"/>
-      <param name="fasta" value="PeptideIndexer_2.fasta"/>
-      <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value=""/>
-      <param name="decoy_string_position" value="prefix"/>
-      <param name="missing_decoy_action" value="error"/>
-      <param name="write_protein_sequence" value="true"/>
-      <param name="write_protein_description" value="false"/>
-      <param name="keep_unreferenced_proteins" value="false"/>
-      <param name="unmatched_action" value="error"/>
-      <param name="aaa_max" value="4"/>
-      <param name="mismatches_max" value="0"/>
-      <param name="IL_equivalent" value="false"/>
-      <section name="enzyme">
-        <param name="name" value="auto"/>
-        <param name="specificity" value="none"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PercolatorAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.5"/>
-        <param name="trainFDR" value="0.5"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PercolatorAdapter_1.idXML"/>
-      <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="out_type" value="idXML"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms2"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.01"/>
-        <param name="trainFDR" value="0.01"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_osw" value="PercolatorAdapter_2.osw"/>
-      <output name="out" file="PercolatorAdapter_2_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <param name="out_type" value="osw"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms1"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.01"/>
-        <param name="trainFDR" value="0.01"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_osw" value="PercolatorAdapter_2_out1.osw"/>
-      <output name="out" file="PercolatorAdapter_3_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <param name="out_type" value="osw"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms2"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.01"/>
-        <param name="trainFDR" value="0.01"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_osw" value="PercolatorAdapter_3_out1.osw"/>
-      <output name="out" file="PercolatorAdapter_4_out1.osw" compare="sim_size" delta="5700" ftype="osw"/>
-      <param name="out_type" value="osw"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="transition"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="generic_feature_set" value="false"/>
-        <param name="subset_max_train" value="0"/>
-        <param name="cpos" value="0.0"/>
-        <param name="cneg" value="0.0"/>
-        <param name="testFDR" value="0.5"/>
-        <param name="trainFDR" value="0.5"/>
-        <param name="maxiter" value="10"/>
-        <param name="nested_xval_bins" value="1"/>
-        <param name="quick_validation" value="false"/>
-        <param name="static" value="false"/>
-        <param name="default_direction" value=""/>
-        <param name="verbose" value="2"/>
-        <param name="unitnorm" value="false"/>
-        <param name="test_each_iteration" value="false"/>
-        <param name="override" value="false"/>
-        <param name="seed" value="1"/>
-        <param name="doc" value="0"/>
-        <param name="klammer" value="false"/>
-        <param name="decoy_pattern" value="random"/>
-        <param name="post_processing_tdc" value="false"/>
-        <param name="train_best_positive" value="false"/>
-        <param name="ipf_max_peakgroup_pep" value="0.7"/>
-        <param name="ipf_max_transition_isotope_overlap" value="0.5"/>
-        <param name="ipf_min_transition_sn" value="0.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PercolatorAdapter_1.idXML"/>
-      <output name="out" file="PercolatorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_pin" file="PercolatorAdapter_1_out1.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="idXML"/>
-      <param name="enzyme" value="trypsin"/>
-      <param name="peptide_level_fdrs" value="false"/>
-      <param name="protein_level_fdrs" value="false"/>
-      <param name="osw_level" value="ms2"/>
-      <param name="score_type" value="q-value"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_pin_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PhosphoScoring">
-</xml>
-  <xml name="autotest_PrecursorIonSelector">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="solver" value="GLPK"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
-      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
-      <param name="num_precursors" value="1"/>
-      <param name="load_preprocessing" value="false"/>
-      <param name="store_preprocessing" value="false"/>
-      <param name="simulation" value="true"/>
-      <output name="sim_results" file="PrecursorIonSelector_1_output.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <section name="algorithm">
-        <param name="type" value="IPS"/>
-        <param name="max_iteration" value="10"/>
-        <param name="rt_bin_capacity" value="10"/>
-        <param name="step_size" value="1"/>
-        <param name="peptide_min_prob" value="0.2"/>
-        <param name="sequential_spectrum_order" value="false"/>
-        <section name="MIPFormulation">
-          <section name="thresholds">
-            <param name="min_protein_probability" value="0.2"/>
-            <param name="min_protein_id_probability" value="0.95"/>
-            <param name="min_pt_weight" value="0.5"/>
-            <param name="min_mz" value="500.0"/>
-            <param name="max_mz" value="5000.0"/>
-            <param name="min_pred_pep_prob" value="0.5"/>
-            <param name="min_rt_weight" value="0.5"/>
-            <param name="use_peptide_rule" value="true"/>
-            <param name="min_peptide_ids" value="2"/>
-            <param name="min_peptide_probability" value="0.95"/>
-          </section>
-          <section name="combined_ilp">
-            <param name="k1" value="0.2"/>
-            <param name="k2" value="0.2"/>
-            <param name="k3" value="0.4"/>
-            <param name="scale_matching_probs" value="true"/>
-          </section>
-          <section name="feature_based">
-            <param name="no_intensity_normalization" value="false"/>
-            <param name="max_number_precursors_per_feature" value="1"/>
-          </section>
-        </section>
-        <section name="Preprocessing">
-          <param name="precursor_mass_tolerance" value="0.9"/>
-          <param name="precursor_mass_tolerance_unit" value="Da"/>
-          <param name="preprocessed_db_path" value=""/>
-          <param name="preprocessed_db_pred_rt_path" value=""/>
-          <param name="preprocessed_db_pred_dt_path" value=""/>
-          <param name="max_peptides_per_run" value="100000"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="taxonomy" value=""/>
-          <param name="store_peptide_sequences" value="false"/>
-          <section name="rt_settings">
-            <param name="min_rt" value="960.0"/>
-            <param name="max_rt" value="3840.0"/>
-            <param name="rt_step_size" value="30.0"/>
-            <param name="gauss_mean" value="-1.0"/>
-            <param name="gauss_sigma" value="3.0"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,sim_results_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="solver" value="GLPK"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PrecursorIonSelector_features.featureXML"/>
-      <output name="out" file="PrecursorIonSelector_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="ids" value="PrecursorIonSelector_ids.idXML"/>
-      <param name="num_precursors" value="1"/>
-      <param name="load_preprocessing" value="false"/>
-      <param name="store_preprocessing" value="false"/>
-      <param name="simulation" value="false"/>
-      <param name="db_path" value="PrecursorIonSelector_db.fasta"/>
-      <param name="fixed_modifications" value=""/>
-      <section name="algorithm">
-        <param name="type" value="IPS"/>
-        <param name="max_iteration" value="10"/>
-        <param name="rt_bin_capacity" value="10"/>
-        <param name="step_size" value="1"/>
-        <param name="peptide_min_prob" value="0.2"/>
-        <param name="sequential_spectrum_order" value="false"/>
-        <section name="MIPFormulation">
-          <section name="thresholds">
-            <param name="min_protein_probability" value="0.2"/>
-            <param name="min_protein_id_probability" value="0.95"/>
-            <param name="min_pt_weight" value="0.5"/>
-            <param name="min_mz" value="500.0"/>
-            <param name="max_mz" value="5000.0"/>
-            <param name="min_pred_pep_prob" value="0.5"/>
-            <param name="min_rt_weight" value="0.5"/>
-            <param name="use_peptide_rule" value="true"/>
-            <param name="min_peptide_ids" value="2"/>
-            <param name="min_peptide_probability" value="0.95"/>
-          </section>
-          <section name="combined_ilp">
-            <param name="k1" value="0.2"/>
-            <param name="k2" value="0.2"/>
-            <param name="k3" value="0.4"/>
-            <param name="scale_matching_probs" value="true"/>
-          </section>
-          <section name="feature_based">
-            <param name="no_intensity_normalization" value="false"/>
-            <param name="max_number_precursors_per_feature" value="1"/>
-          </section>
-        </section>
-        <section name="Preprocessing">
-          <param name="precursor_mass_tolerance" value="0.9"/>
-          <param name="precursor_mass_tolerance_unit" value="Da"/>
-          <param name="preprocessed_db_path" value=""/>
-          <param name="preprocessed_db_pred_rt_path" value=""/>
-          <param name="preprocessed_db_pred_dt_path" value=""/>
-          <param name="max_peptides_per_run" value="100000"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="taxonomy" value=""/>
-          <param name="store_peptide_sequences" value="false"/>
-          <section name="rt_settings">
-            <param name="min_rt" value="960.0"/>
-            <param name="max_rt" value="3840.0"/>
-            <param name="rt_step_size" value="30.0"/>
-            <param name="gauss_mean" value="-1.0"/>
-            <param name="gauss_sigma" value="3.0"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PrecursorMassCorrector">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="max_charge" value="3"/>
-        <param name="intensity_threshold" value="-1.0"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PrecursorMassCorrector_1_input.mzML"/>
-      <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="precursor_mass_tolerance" value="1.5"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ProteinInference">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinInference_1_input.idXML"/>
-      <output name="out" file="ProteinInference_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="merge_runs" value="all"/>
-      <param name="annotate_indist_groups" value="true"/>
-      <section name="Merging">
-        <param name="annotate_origin" value="false"/>
-        <param name="allow_disagreeing_settings" value="false"/>
-      </section>
-      <section name="Algorithm">
-        <param name="min_peptides_per_protein" value="1"/>
-        <param name="score_aggregation_method" value="maximum"/>
-        <param name="treat_charge_variants_separately" value="true"/>
-        <param name="treat_modification_variants_separately" value="true"/>
-        <param name="use_shared_peptides" value="false"/>
-        <param name="skip_count_annotation" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ProteinQuantifier">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="median"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_2_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_2_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="true"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_3_input.featureXML"/>
-      <output name="out" file="ProteinQuantifier_3_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_3_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="2"/>
-      <param name="average" value="mean"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_4_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_5_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_6_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_7_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_8_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_9_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="mztab" file="ProteinQuantifier_9_output_mztab.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,mztab_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_12_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="true"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.consensusXML"/>
-      <output name="out" file="ProteinQuantifier_13_output.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="3"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="true"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="true"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="true"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ProteinQuantifier_input.idXML"/>
-      <output name="out" file="ProteinQuantifier_14_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_out" file="ProteinQuantifier_14_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="top" value="0"/>
-      <param name="average" value="sum"/>
-      <param name="include_all" value="false"/>
-      <param name="best_charge_and_fraction" value="false"/>
-      <param name="greedy_group_resolution" value="false"/>
-      <param name="ratios" value="false"/>
-      <param name="ratiosSILAC" value="false"/>
-      <section name="consensus">
-        <param name="normalize" value="false"/>
-        <param name="fix_peptides" value="false"/>
-      </section>
-      <section name="format">
-        <param name="separator" value=""/>
-        <param name="quoting" value="double"/>
-        <param name="replacement" value="_"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,peptide_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_ProteinResolver">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="fasta" value="ProteinResolver_1_input.fasta"/>
-      <param name="in" value="ProteinResolver_1_input.consensusXML"/>
-      <param name="in_path" value=""/>
-      <output name="protein_groups" file="ProteinResolver_1_output1.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="peptide_table" file="ProteinResolver_1_output2.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="protein_table" file="ProteinResolver_1_output3.txt" compare="sim_size" delta="5700" ftype="csv"/>
-      <section name="resolver">
-        <param name="missed_cleavages" value="2"/>
-        <param name="min_length" value="6"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="designer">
-        <param name="experiment" value="ExperimentalSetting"/>
-        <param name="file" value="File"/>
-        <param name="separator" value="tab"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,protein_groups_FLAG,peptide_table_FLAG,protein_table_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_PSMFeatureExtractor">
-</xml>
-  <xml name="autotest_PTModel">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_positive" value="PTModel_1_input_positive.idXML"/>
-      <param name="in_negative" value="PTModel_1_input_negative.idXML"/>
-      <output name="out" file="PTModel_1_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="c" value="0.5"/>
-      <param name="svm_type" value="C_SVC"/>
-      <param name="nu" value="0.5"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="max_positive_count" value="1000"/>
-      <param name="max_negative_count" value="1000"/>
-      <param name="redundant" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="100.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.1"/>
-        <param name="nu_step_size" value="1.3"/>
-        <param name="nu_stop" value="0.9"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_QCCalculator">
-</xml>
-  <xml name="autotest_QCEmbedder">
-</xml>
-  <xml name="autotest_QCExporter">
-</xml>
-  <xml name="autotest_QCExtractor">
-</xml>
-  <xml name="autotest_QCImporter">
-</xml>
-  <xml name="autotest_QCMerger">
-</xml>
-  <xml name="autotest_QCShrinker">
-</xml>
-  <xml name="autotest_QualityControl">
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_cm" value="QualityControl_1_in.consensusXML"/>
-      <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/>
-      <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
-      <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta="5700" ftype="consensusxml"/>
-      <param name="in_contaminants" value="QualityControl_1.fasta"/>
-      <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
-      <section name="FragmentMassError">
-        <param name="unit" value="auto"/>
-        <param name="tolerance" value="20.0"/>
-      </section>
-      <section name="MS2_id_rate">
-        <param name="assume_all_target" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_RNADigestor">
-</xml>
-  <xml name="autotest_RNAMassCalculator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_seq" value="&quot;AUCGGC&quot;"/>
-      <output name="out" file="RNAMassCalculator_1.txt" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="charge" value="-1 -2"/>
-      <param name="format" value="list"/>
-      <param name="average_mass" value="false"/>
-      <param name="fragment_type" value="full"/>
-      <param name="separator" value=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_RNPxlSearch">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value="Oxidation (M)"/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="1"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value="GUA"/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="false"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="20.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value="Oxidation (M)"/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="1"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value="GUA"/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="true"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="3"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value=""/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="false"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RNPxlSearch_1_input.mzML"/>
-      <param name="database" value="RNPxlSearch_1_input.fasta"/>
-      <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-        <param name="min_charge" value="2"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="10.0"/>
-        <param name="mass_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <section name="peptide">
-        <param name="min_size" value="6"/>
-        <param name="max_size" value="1000000"/>
-        <param name="missed_cleavages" value="1"/>
-        <param name="enzyme" value="Trypsin"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="2"/>
-      </section>
-      <section name="RNPxl">
-        <param name="length" value="2"/>
-        <param name="sequence" value=""/>
-        <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-        <param name="nt_groups" value=""/>
-        <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
-        <param name="can_cross_link" value="U"/>
-        <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
-        <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
-        <param name="scoring" value="fast"/>
-        <param name="decoys" value="true"/>
-        <param name="CysteineAdduct" value="false"/>
-        <param name="filter_fractional_mass" value="false"/>
-        <param name="carbon_labeled_fragments" value="false"/>
-        <param name="only_xl" value="false"/>
-        <param name="filter_small_peptide_mass" value="600.0"/>
-        <param name="marker_ions_tolerance" value="0.05"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_tsv_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_RNPxlXICFilter">
-</xml>
-  <xml name="autotest_RTEvaluation">
-</xml>
-  <xml name="autotest_RTModel">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RTModel_1_input.idXML"/>
-      <output name="out" file="RTModel_1_output.model" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.1"/>
-      <param name="kernel_type" value="POLY"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="total_gradient_time" value="3000.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="10.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.3"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.7"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in_positive" value="RTModel_2_input_positive.idXML"/>
-      <param name="in_negative" value="RTModel_2_input_negative.idXML"/>
-      <output name="out" file="RTModel_2_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.5"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="5.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="true"/>
-        <param name="number_of_runs" value="10"/>
-        <param name="number_of_partitions" value="10"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="1.0"/>
-        <param name="c_step_size" value="10.0"/>
-        <param name="c_stop" value="1000.0"/>
-        <param name="nu_start" value="0.3"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.7"/>
-        <param name="sigma_start" value="1.0"/>
-        <param name="sigma_step_size" value="1.3"/>
-        <param name="sigma_stop" value="15.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RTModel_3_input.idXML"/>
-      <output name="out" file="RTModel_3_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.001953125"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="1.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="false"/>
-        <param name="number_of_runs" value="1"/>
-        <param name="number_of_partitions" value="5"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="0.001953125"/>
-        <param name="c_step_size" value="2.0"/>
-        <param name="c_stop" value="0.001953125"/>
-        <param name="nu_start" value="0.4"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.4"/>
-        <param name="sigma_start" value="5.0"/>
-        <param name="sigma_step_size" value="1.221055"/>
-        <param name="sigma_stop" value="5.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="RTModel_4_input.txt" ftype="txt"/>
-      <output name="out" file="RTModel_4_output.tmp" compare="sim_size" delta="5700" ftype="txt"/>
-      <param name="svm_type" value="NU_SVR"/>
-      <param name="nu" value="0.5"/>
-      <param name="p" value="0.1"/>
-      <param name="c" value="0.001953125"/>
-      <param name="kernel_type" value="OLIGO"/>
-      <param name="degree" value="1"/>
-      <param name="border_length" value="22"/>
-      <param name="max_std" value="10.0"/>
-      <param name="k_mer_length" value="1"/>
-      <param name="sigma" value="1.0"/>
-      <param name="total_gradient_time" value="1.0"/>
-      <param name="first_dim_rt" value="false"/>
-      <param name="additive_cv" value="false"/>
-      <section name="cv">
-        <param name="skip_cv" value="false"/>
-        <param name="number_of_runs" value="1"/>
-        <param name="number_of_partitions" value="5"/>
-        <param name="degree_start" value="1"/>
-        <param name="degree_step_size" value="2"/>
-        <param name="degree_stop" value="4"/>
-        <param name="p_start" value="1.0"/>
-        <param name="p_step_size" value="10.0"/>
-        <param name="p_stop" value="1000.0"/>
-        <param name="c_start" value="0.001953125"/>
-        <param name="c_step_size" value="2.0"/>
-        <param name="c_stop" value="0.001953125"/>
-        <param name="nu_start" value="0.4"/>
-        <param name="nu_step_size" value="1.2"/>
-        <param name="nu_stop" value="0.4"/>
-        <param name="sigma_start" value="5.0"/>
-        <param name="sigma_step_size" value="1.221055"/>
-        <param name="sigma_stop" value="5.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SeedListGenerator">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="PepXMLFile_test.mzML"/>
-      <output name="out" file="SeedListGenerator_1_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="use_peptide_mass" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDMapper_1_output.featureXML"/>
-      <output name="out" file="SeedListGenerator_2_output.featureXML" compare="sim_size" delta="5700" ftype="featurexml"/>
-      <param name="use_peptide_mass" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SemanticValidator">
-</xml>
-  <xml name="autotest_SequenceCoverageCalculator">
-</xml>
-  <xml name="autotest_SimpleSearchEngine">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SimpleSearchEngine_1.mzML"/>
-      <param name="database" value="SimpleSearchEngine_1.fasta"/>
-      <output name="out" file="SimpleSearchEngine_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <section name="Search">
-        <param name="enzyme" value="Trypsin"/>
-        <param name="decoys" value="false"/>
-        <section name="precursor">
-          <param name="mass_tolerance" value="5.0"/>
-          <param name="mass_tolerance_unit" value="ppm"/>
-          <param name="min_charge" value="2"/>
-          <param name="max_charge" value="5"/>
-          <param name="isotopes" value="0 1"/>
-        </section>
-        <section name="fragment">
-          <param name="mass_tolerance" value="0.3"/>
-          <param name="mass_tolerance_unit" value="Da"/>
-        </section>
-        <section name="modifications">
-          <param name="fixed" value=""/>
-          <param name="variable" value="Oxidation (M)"/>
-          <param name="variable_max_per_peptide" value="2"/>
-        </section>
-        <section name="annotate">
-          <param name="PSM" value=""/>
-        </section>
-        <section name="peptide">
-          <param name="min_size" value="7"/>
-          <param name="max_size" value="40"/>
-          <param name="missed_cleavages" value="1"/>
-          <param name="motif" value=""/>
-        </section>
-        <section name="report">
-          <param name="top_hits" value="1"/>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SiriusAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_1_input.mzML"/>
-      <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="3"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_3_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta="5700" ftype="sirius.ms"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_4_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="true"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="all"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="false"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="converter_mode" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SiriusAdapter_2_input.mzML"/>
-      <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
-      <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta="5700" ftype="mztab"/>
-      <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta="5700" ftype="mztab"/>
-      <param name="out_workspace_directory" value=""/>
-      <section name="preprocessing">
-        <param name="filter_by_num_masstraces" value="1"/>
-        <param name="precursor_mz_tolerance" value="0.005"/>
-        <param name="precursor_mz_tolerance_unit" value="Da"/>
-        <param name="precursor_rt_tolerance" value="5"/>
-        <param name="isotope_pattern_iterations" value="3"/>
-        <param name="feature_only" value="false"/>
-        <param name="no_masstrace_info_isotope_pattern" value="false"/>
-      </section>
-      <section name="sirius">
-        <param name="profile" value="qtof"/>
-        <param name="candidates" value="5"/>
-        <param name="database" value="pubchem"/>
-        <param name="noise" value="0"/>
-        <param name="ppm_max" value="10"/>
-        <param name="isotope" value="both"/>
-        <param name="elements" value="CHNOP[5]S[8]Cl[1]"/>
-        <param name="compound_timeout" value="10"/>
-        <param name="tree_timeout" value="0"/>
-        <param name="top_n_hits" value="10"/>
-        <param name="auto_charge" value="true"/>
-        <param name="ion_tree" value="false"/>
-        <param name="no_recalibration" value="false"/>
-        <param name="most_intense_ms2" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpecLibCreator">
-</xml>
-  <xml name="autotest_SpecLibSearcher">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpecLibSearcher_1.mzML"/>
-      <param name="lib" value="SpecLibSearcher_1.MSP"/>
-      <output_collection name="out" count="1"/>
-      <param name="compare_function" value="ZhangSimilarityScore"/>
-      <section name="precursor">
-        <param name="mass_tolerance" value="3.0"/>
-        <param name="mass_tolerance_unit" value="Da"/>
-        <param name="min_charge" value="1"/>
-        <param name="max_charge" value="5"/>
-        <param name="isotopes" value="0 1"/>
-      </section>
-      <section name="fragment">
-        <param name="mass_tolerance" value="10.0"/>
-      </section>
-      <section name="report">
-        <param name="top_hits" value="10"/>
-      </section>
-      <section name="filter">
-        <param name="remove_peaks_below_threshold" value="2.01"/>
-        <param name="min_peaks" value="5"/>
-        <param name="max_peaks" value="150"/>
-        <param name="cut_peaks_below" value="1000"/>
-      </section>
-      <section name="modifications">
-        <param name="fixed" value=""/>
-        <param name="variable" value=""/>
-        <param name="variable_max_per_peptide" value="2"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpectraFilterBernNorm">
-</xml>
-  <xml name="autotest_SpectraFilterMarkerMower">
-</xml>
-  <xml name="autotest_SpectraFilterNLargest">
-</xml>
-  <xml name="autotest_SpectraFilterNormalizer">
-</xml>
-  <xml name="autotest_SpectraFilterParentPeakMower">
-</xml>
-  <xml name="autotest_SpectraFilterScaler">
-</xml>
-  <xml name="autotest_SpectraFilterSqrtMower">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-      <output name="out" file="SpectraFilterSqrtMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpectraFilterThresholdMower">
-</xml>
-  <xml name="autotest_SpectraFilterWindowMower">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpectraFilterWindowMower_1_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="windowsize" value="50.0"/>
-        <param name="peakcount" value="2"/>
-        <param name="movetype" value="slide"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <section name="algorithm">
-        <param name="windowsize" value="20.0"/>
-        <param name="peakcount" value="4"/>
-        <param name="movetype" value="slide"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_SpectraMerger">
-</xml>
-  <xml name="autotest_SpectraSTSearchAdapter"/>
-  <xml name="autotest_StaticModification">
-</xml>
-  <xml name="autotest_SvmTheoreticalSpectrumGeneratorTrainer">
-</xml>
-  <xml name="autotest_TargetedFileConverter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_1_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="minutes"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_2_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="seconds"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_4_input.mrm" ftype="mrm"/>
-      <output name="out" file="ConvertTSVToTraML_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_5_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_5_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_6_input.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_6_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_7_input_Skyline.tsv" ftype="tabular"/>
-      <output name="out" file="ConvertTSVToTraML_7_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_1_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_1_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_2_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_3_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="true"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_3_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_4_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_10_output.TraML.tmp"/>
-      <output name="out" file="TargetedFileConverter_10_output.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_11_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_11_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_8_output.TraML.tmp"/>
-      <output name="out" file="TargetedFileConverter_8_input.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="true"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_9_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_9_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="true"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_output.TraML"/>
-      <output name="out" file="ConvertTraMLToTSV_output.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_12_output.pqp.tmp"/>
-      <output name="out" file="TargetedFileConverter_12_input.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="true"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TargetedFileConverter_12_input.tsv" ftype="tabular"/>
-      <output name="out" file="TargetedFileConverter_13_output.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="TraML"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="ConvertTSVToTraML_5_output.TraML"/>
-      <output name="out" file="ConvertTraMLToTSV_output_2.tmp.tsv" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="out_type" value="tsv"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="legacy_traml_id" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" ftype="tabular"/>
-      <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus_traml.tmp.TraML" compare="sim_size" delta="5700" ftype="traml"/>
-      <param name="out_type" value="traml"/>
-      <section name="algorithm">
-        <param name="retentionTimeInterpretation" value="iRT"/>
-        <param name="override_group_label_check" value="false"/>
-        <param name="force_invalid_mods" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TextExporter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="5">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_2_input.consensusXML"/>
-      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="true"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="RT_then_MZ"/>
-        <param name="sort_by_maps" value="true"/>
-        <param name="sort_by_size" value="true"/>
-      </section>
-      <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta="5700" ftype="csv"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="true"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_5_input.idXML"/>
-      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="true"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="true"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_6_input.featureXML"/>
-      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="true"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_7_input.consensusXML"/>
-      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="RT_then_MZ"/>
-        <param name="sort_by_maps" value="true"/>
-        <param name="sort_by_size" value="true"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="true"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-        <param name="add_hit_metavalues" value="-1"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TextExporter_9_input.idXML"/>
-      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta="5700" ftype="tabular"/>
-      <param name="separator" value=""/>
-      <param name="replacement" value="_"/>
-      <param name="quoting" value="none"/>
-      <param name="no_ids" value="false"/>
-      <section name="feature">
-        <param name="minimal" value="false"/>
-        <param name="add_metavalues" value="-1"/>
-      </section>
-      <section name="id">
-        <param name="proteins_only" value="false"/>
-        <param name="peptides_only" value="false"/>
-        <param name="protein_groups" value="false"/>
-        <param name="first_dim_rt" value="false"/>
-        <param name="add_metavalues" value="0"/>
-        <param name="add_hit_metavalues" value="0"/>
-        <param name="add_protein_hit_metavalues" value="-1"/>
-      </section>
-      <section name="consensus">
-        <param name="sorting_method" value="none"/>
-        <param name="sort_by_maps" value="false"/>
-        <param name="sort_by_size" value="false"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TICCalculator">
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="regular"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="streaming"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="streaming"/>
-      <param name="loadData" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="indexed"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MapNormalizer_output.mzML"/>
-      <param name="read_method" value="indexed_parallel"/>
-      <param name="loadData" value="true"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TOFCalibration">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TOFCalibration_1_input.mzML"/>
-      <output name="out" file="TOFCalibration_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ext_calibrants" value="TOFCalibration_1_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
-      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
-      <param name="peak_data" value="false"/>
-      <section name="algorithm">
-        <section name="PeakPicker">
-          <param name="signal_to_noise" value="3.0"/>
-          <param name="centroid_percentage" value="0.6"/>
-          <param name="peak_width" value="0.15"/>
-          <param name="estimate_peak_width" value="false"/>
-          <param name="fwhm_lower_bound_factor" value="0.7"/>
-          <param name="fwhm_upper_bound_factor" value="20.0"/>
-          <section name="optimization">
-            <param name="iterations" value="400"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="left_width" value="1.0"/>
-              <param name="right_width" value="1.0"/>
-              <param name="height" value="1.0"/>
-            </section>
-            <section name="2d">
-              <param name="tolerance_mz" value="2.2"/>
-              <param name="max_peak_distance" value="1.2"/>
-            </section>
-          </section>
-          <section name="thresholds">
-            <param name="peak_bound" value="400.0"/>
-            <param name="peak_bound_ms2_level" value="10.0"/>
-            <param name="correlation" value="0.0"/>
-            <param name="noise_level" value="0.1"/>
-            <param name="search_radius" value="3"/>
-          </section>
-          <section name="wavelet_transform">
-            <param name="spacing" value="0.001"/>
-          </section>
-          <section name="deconvolution">
-            <param name="deconvolution" value="false"/>
-            <param name="asym_threshold" value="0.3"/>
-            <param name="left_width" value="2.0"/>
-            <param name="right_width" value="2.0"/>
-            <param name="scaling" value="0.12"/>
-            <section name="fitting">
-              <param name="fwhm_threshold" value="0.7"/>
-              <param name="eps_abs" value="9.999999747378752e-06"/>
-              <param name="eps_rel" value="9.999999747378752e-06"/>
-              <param name="max_iteration" value="10"/>
-              <section name="penalties">
-                <param name="position" value="0.0"/>
-                <param name="height" value="1.0"/>
-                <param name="left_width" value="0.0"/>
-                <param name="right_width" value="0.0"/>
-              </section>
-            </section>
-          </section>
-          <section name="SignalToNoiseEstimationParameter">
-            <param name="max_intensity" value="-1"/>
-            <param name="auto_max_stdev_factor" value="3.0"/>
-            <param name="auto_max_percentile" value="95"/>
-            <param name="auto_mode" value="0"/>
-            <param name="win_len" value="200.0"/>
-            <param name="bin_count" value="30"/>
-            <param name="stdev_mp" value="3.0"/>
-            <param name="min_required_elements" value="10"/>
-            <param name="noise_for_empty_window" value="1e+20"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="TOFCalibration_2_input.mzML"/>
-      <output name="out" file="TOFCalibration_2_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-      <param name="ext_calibrants" value="TOFCalibration_2_calibrants.mzML"/>
-      <param name="ref_masses" value="TOFCalibration_ref_masses.tsv" ftype="tabular"/>
-      <param name="tof_const" value="TOFCalibration_const.tsv" ftype="tabular"/>
-      <param name="peak_data" value="true"/>
-      <section name="algorithm">
-        <section name="PeakPicker">
-          <param name="signal_to_noise" value="3.0"/>
-          <param name="centroid_percentage" value="0.6"/>
-          <param name="peak_width" value="0.15"/>
-          <param name="estimate_peak_width" value="false"/>
-          <param name="fwhm_lower_bound_factor" value="0.7"/>
-          <param name="fwhm_upper_bound_factor" value="20.0"/>
-          <section name="optimization">
-            <param name="iterations" value="400"/>
-            <section name="penalties">
-              <param name="position" value="0.0"/>
-              <param name="left_width" value="1.0"/>
-              <param name="right_width" value="1.0"/>
-              <param name="height" value="1.0"/>
-            </section>
-            <section name="2d">
-              <param name="tolerance_mz" value="2.2"/>
-              <param name="max_peak_distance" value="1.2"/>
-            </section>
-          </section>
-          <section name="thresholds">
-            <param name="peak_bound" value="400.0"/>
-            <param name="peak_bound_ms2_level" value="10.0"/>
-            <param name="correlation" value="0.0"/>
-            <param name="noise_level" value="0.1"/>
-            <param name="search_radius" value="3"/>
-          </section>
-          <section name="wavelet_transform">
-            <param name="spacing" value="0.001"/>
-          </section>
-          <section name="deconvolution">
-            <param name="deconvolution" value="false"/>
-            <param name="asym_threshold" value="0.3"/>
-            <param name="left_width" value="2.0"/>
-            <param name="right_width" value="2.0"/>
-            <param name="scaling" value="0.12"/>
-            <section name="fitting">
-              <param name="fwhm_threshold" value="0.7"/>
-              <param name="eps_abs" value="9.999999747378752e-06"/>
-              <param name="eps_rel" value="9.999999747378752e-06"/>
-              <param name="max_iteration" value="10"/>
-              <section name="penalties">
-                <param name="position" value="0.0"/>
-                <param name="height" value="1.0"/>
-                <param name="left_width" value="0.0"/>
-                <param name="right_width" value="0.0"/>
-              </section>
-            </section>
-          </section>
-          <section name="SignalToNoiseEstimationParameter">
-            <param name="max_intensity" value="-1"/>
-            <param name="auto_max_stdev_factor" value="3.0"/>
-            <param name="auto_max_percentile" value="95"/>
-            <param name="auto_mode" value="0"/>
-            <param name="win_len" value="200.0"/>
-            <param name="bin_count" value="30"/>
-            <param name="stdev_mp" value="3.0"/>
-            <param name="min_required_elements" value="10"/>
-            <param name="noise_for_empty_window" value="1e+20"/>
-          </section>
-        </section>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_TransformationEvaluation">
-</xml>
-  <xml name="autotest_XFDR">
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in1.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out1_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out1_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out1_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in1.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out2_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out2_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out2_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="true"/>
-      <param name="no_qvalues" value="true"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out3_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out3_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out3_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="0.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out4_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out4_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out4_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-3.0"/>
-      <param name="maxborder" value="3.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in3.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out5_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out5_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out5_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-3.0"/>
-      <param name="maxborder" value="3.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in4.idXML"/>
-      <output name="out_idXML" file="XFDR_test_out6_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="false"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="-10.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="4">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="XFDR_test_in2.xquest.xml"/>
-      <output name="out_idXML" file="XFDR_test_out7_temp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="out_mzIdentML" file="XFDR_test_out7_temp.mzid" compare="sim_size" delta="5700" ftype="mzid"/>
-      <output name="out_xquest" file="XFDR_test_out7_temp.xquest.xml" compare="sim_size" delta="5700" ftype="xquest.xml"/>
-      <param name="decoy_string" value="DECOY_"/>
-      <param name="minborder" value="-50.0"/>
-      <param name="maxborder" value="50.0"/>
-      <param name="mindeltas" value="0.0"/>
-      <param name="minionsmatched" value="0"/>
-      <param name="uniquexl" value="true"/>
-      <param name="no_qvalues" value="false"/>
-      <param name="minscore" value="0.0"/>
-      <param name="binsize" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_idXML_FLAG,out_mzIdentML_FLAG,out_xquest_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-  <xml name="autotest_XMLValidator">
-</xml>
-  <xml name="autotest_XTandemAdapter">
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
-      <param name="ignore_adapter_param" value="false"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="max_precursor_charge" value="0"/>
-      <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="minimum_fragment_mz" value="150.0"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="semi_cleavage" value="false"/>
-      <param name="output_results" value="all"/>
-      <param name="max_valid_expect" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_2_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
-      <param name="ignore_adapter_param" value="false"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="max_precursor_charge" value="0"/>
-      <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="minimum_fragment_mz" value="150.0"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="semi_cleavage" value="false"/>
-      <param name="output_results" value="valid"/>
-      <param name="max_valid_expect" value="1e-14"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="XTandemAdapter_3_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteinslong.fasta"/>
-      <param name="default_config_file" value="CHEMISTRY/XTandem_default_input.xml"/>
-      <param name="ignore_adapter_param" value="false"/>
-      <param name="precursor_mass_tolerance" value="5.0"/>
-      <param name="fragment_mass_tolerance" value="0.3"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="fragment_error_units" value="Da"/>
-      <param name="max_precursor_charge" value="0"/>
-      <param name="no_isotope_error" value="false"/>
-      <param name="fixed_modifications" value=""/>
-      <param name="variable_modifications" value="Oxidation (M)"/>
-      <param name="minimum_fragment_mz" value="150.0"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="missed_cleavages" value="1"/>
-      <param name="semi_cleavage" value="false"/>
-      <param name="output_results" value="all"/>
-      <param name="max_valid_expect" value="0.1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-  </xml>
-<xml name="autotest_PTPredict"/><xml name="autotest_InclusionExclusionListCreator"/><xml name="autotest_RTPredict"/><xml name="autotest_ProteomicsLFQ"/><xml name="autotest_IDDecoyProbability"/><xml name="autotest_InspectAdapter"/></macros>
diff -r aa43ad3b2da6 -r aa8658367608 macros_discarded_auto.xml
--- a/macros_discarded_auto.xml	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,378 +0,0 @@
-
-<xml name="manutest_OpenSwathFileSplitter">
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-  <output_collection name="outputDirectory" count=""/>
-  <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_qc_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test></xml>
-<xml name="manutest_IDRipper">
-<test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDRipper_1_input.idXML"/>
-      <output_collection name="out_path" count=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test><test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDRipper_2_input.idXML"/>
-      <output_collection name="out_path" count=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test><test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="IDRipper_3_output.idXML"/>
-      <output_collection name="out_path" count=""/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test></xml>
-<xml name="manutest_MzMLSplitter">
-<test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output_collection name="out" count=""/>
-      <param name="parts" value="2"/>
-      <param name="size" value="0"/>
-      <param name="unit" value="MB"/>
-      <param name="no_chrom" value="false"/>
-      <param name="no_spec" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test><test expect_num_outputs="1">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="FileFilter_1_input.mzML"/>
-      <output_collection name="out" count=""/>
-      <param name="parts" value="1"/>
-      <param name="size" value="40"/>
-      <param name="unit" value="KB"/>
-      <param name="no_chrom" value="false"/>
-      <param name="no_spec" value="false"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test></xml>
-<xml name="manutest_MSFraggerAdapter">
-<test expect_num_outputs="3">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="java_heapmemory" value="2600"/>
-      <param name="in" value="spectra.mzML"/>
-      <output name="out" file="MSFraggerAdapter_7_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <output name="opt_out" file="MSFraggerAdapter_7_opt_out_tmp.pepXML" compare="sim_size" delta="5700" ftype="pepxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <section name="tolerance">
-        <param name="precursor_mass_tolerance" value="20.0"/>
-        <param name="precursor_mass_unit" value="ppm"/>
-        <param name="precursor_true_tolerance" value="0.0"/>
-        <param name="precursor_true_unit" value="ppm"/>
-        <param name="fragment_mass_tolerance" value="20.0"/>
-        <param name="fragment_mass_unit" value="ppm"/>
-        <param name="isotope_error" value="0"/>
-      </section>
-      <section name="digest">
-        <param name="search_enzyme_name" value="Trypsin"/>
-        <param name="search_enzyme_cutafter" value="KR"/>
-        <param name="search_enzyme_nocutbefore" value="P"/>
-        <param name="num_enzyme_termini" value="semi"/>
-        <param name="allowed_missed_cleavage" value="2"/>
-        <param name="min_length" value="7"/>
-        <param name="max_length" value="64"/>
-        <param name="mass_range_min" value="500.0"/>
-        <param name="mass_range_max" value="5000.0"/>
-      </section>
-      <section name="varmod">
-        <param name="clip_nterm_m" value="false"/>
-        <param name="masses" value=""/>
-        <param name="syntaxes" value=""/>
-        <param name="enable_common" value="true"/>
-        <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
-        <param name="max_variable_mods_per_mod" value="2"/>
-        <param name="max_variable_mods_combinations" value="5000"/>
-      </section>
-      <section name="spectrum">
-        <param name="minimum_peaks" value="10"/>
-        <param name="use_topn_peaks" value="50"/>
-        <param name="minimum_ratio" value="0.0"/>
-        <param name="clear_mz_range_min" value="0.0"/>
-        <param name="clear_mz_range_max" value="0.0"/>
-        <param name="max_fragment_charge" value="2"/>
-        <param name="override_charge" value="false"/>
-        <param name="precursor_charge_min" value="1"/>
-        <param name="precursor_charge_max" value="4"/>
-      </section>
-      <section name="search">
-        <param name="track_zero_topn" value="0"/>
-        <param name="zero_bin_accept_expect" value="0.0"/>
-        <param name="zero_bin_mult_expect" value="1.0"/>
-        <param name="add_topn_complementary" value="0"/>
-        <param name="min_fragments_modeling" value="3"/>
-        <param name="min_matched_fragments" value="4"/>
-        <param name="output_report_topn" value="1"/>
-        <param name="output_max_expect" value="50.0"/>
-      </section>
-      <section name="statmod">
-        <param name="add_cterm_peptide" value="0.0"/>
-        <param name="add_nterm_peptide" value="0.0"/>
-        <param name="add_cterm_protein" value="0.0"/>
-        <param name="add_nterm_protein" value="0.0"/>
-        <param name="add_G_glycine" value="0.0"/>
-        <param name="add_A_alanine" value="0.0"/>
-        <param name="add_S_serine" value="0.0"/>
-        <param name="add_P_proline" value="0.0"/>
-        <param name="add_V_valine" value="0.0"/>
-        <param name="add_T_threonine" value="0.0"/>
-        <param name="add_C_cysteine" value="57.021464"/>
-        <param name="add_L_leucine" value="0.0"/>
-        <param name="add_I_isoleucine" value="0.0"/>
-        <param name="add_N_asparagine" value="0.0"/>
-        <param name="add_D_aspartic_acid" value="0.0"/>
-        <param name="add_Q_glutamine" value="0.0"/>
-        <param name="add_K_lysine" value="0.0"/>
-        <param name="add_E_glutamic_acid" value="0.0"/>
-        <param name="add_M_methionine" value="0.0"/>
-        <param name="add_H_histidine" value="0.0"/>
-        <param name="add_F_phenylalanine" value="0.0"/>
-        <param name="add_R_arginine" value="0.0"/>
-        <param name="add_Y_tyrosine" value="0.0"/>
-        <param name="add_W_tryptophan" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,opt_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test><test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="java_heapmemory" value="2600"/>
-      <param name="in" value="spectra_comet.mzML"/>
-      <output name="out" file="MSFraggerAdapter_8_out_tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="database" value="proteins.fasta"/>
-      <section name="tolerance">
-        <param name="precursor_mass_tolerance" value="20.0"/>
-        <param name="precursor_mass_unit" value="ppm"/>
-        <param name="precursor_true_tolerance" value="0.0"/>
-        <param name="precursor_true_unit" value="ppm"/>
-        <param name="fragment_mass_tolerance" value="20.0"/>
-        <param name="fragment_mass_unit" value="ppm"/>
-        <param name="isotope_error" value="0"/>
-      </section>
-      <section name="digest">
-        <param name="search_enzyme_name" value="Trypsin"/>
-        <param name="search_enzyme_cutafter" value="KR"/>
-        <param name="search_enzyme_nocutbefore" value="P"/>
-        <param name="num_enzyme_termini" value="semi"/>
-        <param name="allowed_missed_cleavage" value="2"/>
-        <param name="min_length" value="7"/>
-        <param name="max_length" value="64"/>
-        <param name="mass_range_min" value="500.0"/>
-        <param name="mass_range_max" value="5000.0"/>
-      </section>
-      <section name="varmod">
-        <param name="clip_nterm_m" value="false"/>
-        <param name="masses" value=""/>
-        <param name="syntaxes" value=""/>
-        <param name="enable_common" value="true"/>
-        <param name="not_allow_multiple_variable_mods_on_residue" value="false"/>
-        <param name="max_variable_mods_per_mod" value="2"/>
-        <param name="max_variable_mods_combinations" value="5000"/>
-      </section>
-      <section name="spectrum">
-        <param name="minimum_peaks" value="10"/>
-        <param name="use_topn_peaks" value="50"/>
-        <param name="minimum_ratio" value="0.0"/>
-        <param name="clear_mz_range_min" value="0.0"/>
-        <param name="clear_mz_range_max" value="0.0"/>
-        <param name="max_fragment_charge" value="2"/>
-        <param name="override_charge" value="false"/>
-        <param name="precursor_charge_min" value="1"/>
-        <param name="precursor_charge_max" value="4"/>
-      </section>
-      <section name="search">
-        <param name="track_zero_topn" value="0"/>
-        <param name="zero_bin_accept_expect" value="0.0"/>
-        <param name="zero_bin_mult_expect" value="1.0"/>
-        <param name="add_topn_complementary" value="0"/>
-        <param name="min_fragments_modeling" value="3"/>
-        <param name="min_matched_fragments" value="4"/>
-        <param name="output_report_topn" value="1"/>
-        <param name="output_max_expect" value="50.0"/>
-      </section>
-      <section name="statmod">
-        <param name="add_cterm_peptide" value="0.0"/>
-        <param name="add_nterm_peptide" value="0.0"/>
-        <param name="add_cterm_protein" value="0.0"/>
-        <param name="add_nterm_protein" value="0.0"/>
-        <param name="add_G_glycine" value="0.0"/>
-        <param name="add_A_alanine" value="0.0"/>
-        <param name="add_S_serine" value="0.0"/>
-        <param name="add_P_proline" value="0.0"/>
-        <param name="add_V_valine" value="0.0"/>
-        <param name="add_T_threonine" value="0.0"/>
-        <param name="add_C_cysteine" value="57.021464"/>
-        <param name="add_L_leucine" value="0.0"/>
-        <param name="add_I_isoleucine" value="0.0"/>
-        <param name="add_N_asparagine" value="0.0"/>
-        <param name="add_D_aspartic_acid" value="0.0"/>
-        <param name="add_Q_glutamine" value="0.0"/>
-        <param name="add_K_lysine" value="0.0"/>
-        <param name="add_E_glutamic_acid" value="0.0"/>
-        <param name="add_M_methionine" value="0.0"/>
-        <param name="add_H_histidine" value="0.0"/>
-        <param name="add_F_phenylalanine" value="0.0"/>
-        <param name="add_R_arginine" value="0.0"/>
-        <param name="add_Y_tyrosine" value="0.0"/>
-        <param name="add_W_tryptophan" value="0.0"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test></xml>
-<xml name="manutest_MaRaClusterAdapter">
-<test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="verbose" value="2"/>
-        <param name="precursor_tolerance" value="20.0"/>
-        <param name="precursor_tolerance_units" value="ppm"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="MaRaClusterAdapter_1_in_1.mzML,MaRaClusterAdapter_1_in_2.mzML"/>
-      <param name="id_in" value="MaRaClusterAdapter_1_in_3.idXML"/>
-      <output name="out" file="MaRaClusterAdapter_2_out_1.tmp.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="pcut" value="-10.0"/>
-      <param name="min_cluster_size" value="1"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test></xml>
-<xml name="manutest_NovorAdapter">
-<test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="in" value="NovorAdapter_in.mzML"/>
-      <output name="out" file="NovorAdapter_1_out.idXML" compare="sim_size" delta="5700" ftype="idxml"/>
-      <param name="enzyme" value="Trypsin"/>
-      <param name="fragmentation" value="CID"/>
-      <param name="massAnalyzer" value="Trap"/>
-      <param name="fragment_mass_tolerance" value="0.5"/>
-      <param name="precursor_mass_tolerance" value="15.0"/>
-      <param name="precursor_error_units" value="ppm"/>
-      <param name="variable_modifications" value="Acetyl (K)"/>
-      <param name="fixed_modifications" value="Carbamidomethyl (C)"/>
-      <param name="forbiddenResidues" value="I"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test></xml>
-<xml name="manutest_SpectraSTSearchAdapter">
-<test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_isotopically_averaged_mass" value="false"/>
-        <param name="use_all_charge_states" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
-      <param name="output_files_type" value="pep.xml"/>
-      <output_collection name="output_files" count="1"/>
-      <param name="library_file" value="testLib.splib" ftype="splib"/>
-      <param name="sequence_database_type" value="AA"/>
-      <param name="precursor_mz_tolerance" value="3.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test><test expect_num_outputs="2">
-      <conditional name="adv_opts_cond">
-        <param name="adv_opts_selector" value="advanced"/>
-        <param name="use_isotopically_averaged_mass" value="false"/>
-        <param name="use_all_charge_states" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </conditional>
-      <param name="spectra_files" value="SpectrastAdapter_1_hack.mzML"/>
-      <param name="output_files_type" value="tsv"/>
-      <output_collection name="output_files" count="1"/>
-      <param name="library_file" value="testLib.splib" ftype="splib"/>
-      <param name="sequence_database_type" value="AA"/>
-      <param name="precursor_mz_tolerance" value="3.0"/>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test></xml>
diff -r aa43ad3b2da6 -r aa8658367608 macros_test.xml
--- a/macros_test.xml	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,545 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<macros>
-    
-<!-- a copy of a FileConverter test without the advanced options used
-     in order to check if this works (all other tests enable advanced) -->
-<xml name="manutest_FileConverter">
-<test expect_num_outputs="1">
-  <param name="in" value="FileConverter_1_input.mzData"/>
-  <output name="out" file="FileConverter_1_output.mzML" compare="sim_size" delta="5700" ftype="mzml"/>
-  <param name="out_type" value="mzML"/>
-</test>
-</xml>
-<!-- tests contributed by the galaxyproteomics community -->
-<xml name="manutest_ClusterMassTracesByPrecursor">
-  <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in_ms1" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <param name="in_swath" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTracesByPrecursor.mzml"/>
-  </test>
-</xml>
-<xml name="manutest_ClusterMassTraces"> 
-  <test expect_num_outputs="1"><!-- test with arbitarily chosen consensusXML -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusMapNormalizer_input.consensusXML"/>
-    <output name="out" ftype="mzml" value="ClusterMassTraces.mzml"/>
-  </test>
-</xml>
-<xml name="manutest_CVInspector">
-  <!-- test with https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/cv/XLMOD.obo listed here https://www.psidev.info/groups/controlled-vocabularies, mapping file from share/OpenMS/MAPPING/ms-mapping.xml, see currently not working, see: https://github.com/OpenMS/OpenMS/pull/4425 -->
-  <test expect_num_outputs="1">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="cv_files" ftype="obo" value="CHEMISTRY/XLMOD.obo"/>
-    <param name="cv_names" value="XLMOD"/>
-    <param name="mapping_file" value="MAPPING/ms-mapping.xml"/>
-    <param name="OPTIONAL_OUTPUTS" value="html_FLAG"/>
-    <output name="html" ftype="html" value="CVInspector.html"/>
-  </test>
-</xml>
-<xml name="manutest_DeMeanderize">
-  <test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
-	<output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
-  </test>
-</xml>
-<xml name="manutest_Digestor">
-  <test expect_num_outputs="1"><!-- just using some random fasta, in contrast to DigestorMotif idXML/fasta output possible, testing for the non-default fasta option -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="random.fa"/>
-    <output name="out" ftype="fasta" value="Digestor.fasta"/>
-    <param name="out_type" value="fasta"/>
-  </test>
-</xml>
-<xml name="manutest_EICExtractor">
-  <test expect_num_outputs="1"><!-- just using some random test data -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="spectra.mzML"/>
-    <param name="pos" ftype="edta" value="FileConverter_10_input.edta"/>
-    <output name="out" ftype="csv" value="EICExtractor.csv" lines_diff="2"/>
-  </test>
-</xml>
-<xml name="manutest_ERPairFinder">
-  <!-- TODO -->
-</xml>
-<xml name="manutest_FeatureFinderIsotopeWavelet">
-  <test expect_num_outputs="1"><!--just use the input of another FeatureFinder -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_input.mzML"/>
-    <output name="out" value="FeatureFinderIsotopeWavelet.featureXML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_FFEval">
-  <test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
-    <output name="out" value="FFEval.featureXML" compare="sim_size"/>
-	<output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
-  </test>
-</xml>
-<xml name="manutest_IDExtractor">
-  <test expect_num_outputs="1"><!--  -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="best_hits" value="true"/>
-    <param name="number_of_peptides" value="1"/>
-    <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
-  </test>
-</xml>
-<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
-<xml name="manutest_IDRipper"> 
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="IDRipper_1_input.idXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output_collection name="out_path" count="2">
-    <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
-    <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
-  </output_collection>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="IDRipper_2_input.idXML"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output_collection name="out_path" count="2">
-    <element name="IDRipper_2_output1" file="IDRipper_2_output1.idXML" ftype="idxml"/>
-    <element name="IDRipper_2_output2" file="IDRipper_2_output2.idXML" ftype="idxml"/>
-  </output_collection>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="IDRipper_3_output.idXML"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output_collection name="out_path" count="2">
-    <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/>
-    <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/>
-  </output_collection>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-</test>
-</xml>
-<xml name="manutest_LabeledEval">
-  <test expect_num_outputs="1"><!-- comparing an arbitarty featureXML that has a corresponding consensusXML -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
-    <param name="truth" value="FeatureLinkerLabeled_1_output.consensusXML"/>
-    <output name="stdout" value="LabeledEval.txt" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_MapStatistics">
-  <test expect_num_outputs="1"><!-- test with a featureXML input  -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
-    <output name="out" ftype="txt" value="MapStatistics.txt"/>
-  </test>
-  <test expect_num_outputs="1"><!-- test with a consensusxml input -->
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
-    <output name="out" ftype="txt" value="MapStatistics2.txt"/>
-  </test>
-</xml>
-<xml name="manutest_MetaboliteSpectralMatcher">
-    <!-- same input as used in the MSGF+Adapter, should use database CHEMISTRY/MetaboliteSpectralDB.mzML -->
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter, used as input and database -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="database" value="MetaboliteSpectralDB.mzML"/>
-    <output name="out" ftype="mztab" value="MetaboliteSpectralMatcher.mzTab"/>
-  </test>
-</xml>
-<xml name="manutest_MRMPairFinder">
-  <!-- TODO no idea about a useful input for pair_in -->
-</xml>
-<xml name="manutest_MSSimulator">
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter generate MALDI output for use in the test for DeMeanderize -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="DecoyDatabase_1.fasta"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="mzml" value="MSsimulator_MALDI.mzml" compare="sim_size" delta="1000000" delta_frac="0.1"/>
-    <param name="algorithm|RandomNumberGenerators|biological" value="reproducible"/>
-    <param name="algorithm|RandomNumberGenerators|technical" value="reproducible"/>
-    <param name="algorithm|MSSim|Global|ionization_type" value="MALDI"/>
-  </test>
-</xml>
-<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
-<xml name="manutest_MzMLSplitter">
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="2"/>
-  <param name="size" value="0"/>
-  <param name="unit" value="MB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-<test expect_num_outputs="2">
-  <conditional name="adv_opts_cond">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="force" value="false"/>
-    <param name="test" value="true"/>
-  </conditional>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="1"/>
-  <param name="size" value="40"/>
-  <param name="unit" value="KB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-</xml>
-<xml name="manutest_OpenSwathDIAPreScoring">
-  <!-- data from a test that included all the needed test files -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-    <output_collection name="output_files" count="1">
-      <element name="OpenSwathAnalyzer_2_swathfile_mzML.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-  
-  <!-- test with two inputs (actually the same file .. symlinked) -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
-    <output_collection name="output_files" count="2">
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-      <element name="OpenSwathDIAPreScoring_in1.tsv" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-</xml>
-<!-- adapted from macros_discarded_auto.xml (due to prefix-output)-->
-<xml name="manutest_OpenSwathFileSplitter">
-  <test expect_num_outputs="3">
-    <conditional name="adv_opts_cond">
-      <param name="adv_opts_selector" value="advanced"/>
-      <param name="force" value="false"/>
-      <param name="test" value="true"/>
-    </conditional>
-    <param name="in" value="OpenSwathWorkflow_1_input.mzML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_qc_FLAG,ctd_out_FLAG"/>
-    <output_collection name="outputDirectory" count="6">
-      <element name="OpenSwathWorkflow_1_input_mzML_4" file="openswath_tmpfile_4.mzML" ftype="mzml"/>
-      <element name="OpenSwathWorkflow_1_input_mzML_ms1" file="openswath_tmpfile_ms1.mzML" ftype="mzml"/>
-    </output_collection>
-    <output name="out_qc" file="OpenSwathFileSplitter_1.json" compare="sim_size" delta="5700" ftype="json"/>
-    <output name="ctd_out" ftype="xml">
-      <assert_contents>
-        <is_valid_xml/>
-      </assert_contents>
-    </output>
-  </test>
-</xml>
-<xml name="manutest_OpenSwathRewriteToFeatureXML">
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="featureXML" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <output name="out" ftype="featurexml" value="OpenSwathRewriteToFeatureXML.featureXML"/>
-  </test>
-</xml>
-<xml name="manutest_PepNovoAdapter">
-  <test expect_num_outputs="1"><!-- adapted from (dysfunctional) OMS 3rdParty tests (but model selection
-             unclear https://github.com/OpenMS/OpenMS/issues/4719)-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="PepNovo_1.mzML"/>
-    <output name="out" ftype="idxml" value="PepNovoAdapter_3_output.idXML"/>
-    <param name="model" value="LTQ_COMP"/>
-  </test>
-</xml>
-<xml name="manutest_PhosphoScoring">
-  <test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
-    <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
-  </test>
-</xml>
-<xml name="manutest_PSMFeatureExtractor">
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|skip_db_check" value="true"/>
-    <param name="out_type" value="idxml"/>
-    <output name="out" ftype="idxml" value="PSMFeatureExtractor.idxml" compare="sim_size" delta="500"/>
-  </test>
-  <test expect_num_outputs="1"><!-- using the idXML outputs of two SearchAdapters that should be compatible -->
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML,XTandemAdapter_1_out.idXML"/>
-    <param name="multiple_search_engines" value="true"/>
-    <param name="adv_opts_cond|adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|skip_db_check" value="true"/>
-    <param name="out_type" value="mzid"/>
-    <output name="out" ftype="mzid" value="PSMFeatureExtractor.mzid" compare="sim_size" delta="500"/>
-  </test>
-</xml>
-<xml name="manutest_QCCalculator">
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
-    <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
-    <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
-    <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
-    <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
-    <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
-  </test>
-</xml>
-<xml name="manutest_QCEmbedder">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCExporter">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCExtractor">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCImporter">
-    <!--TODO-->
-</xml>
-<xml name="manutest_QCMerger">
-  <test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
-    <output name="out" ftype="qcml" value="QCMerger.qcML"/>
-  </test>
-</xml>
-<xml name="manutest_QCShrinker">
-  <test expect_num_outputs="1"><!-- just using an output of QCCalculator as input  -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
-    <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
-  </test>
-</xml>
-<xml name="manutest_RNADigestor">
-  <test expect_num_outputs="1"><!--random RNAsequence input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="fasta" value="random_RNA.fa"/>
-    <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
-  </test>
-</xml>
-<xml name="manutest_RNPxlXICFilter">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
-  </test>
-</xml>
-<xml name="manutest_RTEvaluation">
-  <!-- just chosen an arbitrary input and autgenerated output-->
-  <test expect_num_outputs="1">
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="idxml" value="PeptideIndexer_1.idXML"/>
-    <output name="out" ftype="tabular" value="RTEvaluation.tsv"/>
-  </test>
-</xml>
-<xml name="manutest_SemanticValidator">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input (same as XMLValidator) and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <param name="mapping_file" ftype="xml" value="MAPPING/ms-mapping.xml"/>
-    <output name="stdout" ftype="txt" value="SemanticValidator.stdout" lines_diff="4">
-       <assert_contents><has_text text="Congratulations, the file is valid!"/></assert_contents>
-    </output>
-  </test>
-</xml>
-<xml name="manutest_SequenceCoverageCalculator">
-  <test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
-    <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
-    <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpecLibCreator">
-  <!--TODO could not find test data -->
-</xml>
-<xml name="manutest_SpectraFilterBernNorm">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterBernNorm.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterMarkerMower">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterMarkerMower.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterNLargest">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterNLargest.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterNormalizer">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterParentPeakMower">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterScaler">
-  <test expect_num_outputs="1"> <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterScaler.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraFilterThresholdMower">
-  <test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SpectraMerger">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
-    <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
-  </test>
-</xml>
-<xml name="manutest_SvmTheoreticalSpectrumGeneratorTrainer">
-<!-- -TODO model_output_file creates multiple files-->
-</xml>
-<xml name="manutest_TransformationEvaluation">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="trafoxml" value="FileInfo_16_input.trafoXML"/>
-    <param name="OPTIONAL_OUTPUTS" value="out_FLAG"/>
-    <output name="out" ftype="trafoxml" value="TransformationEvaluation.trafoXML" compare="sim_size" delta="100000000"/>
-  </test>
-</xml>
-<xml name="manutest_XMLValidator">
-  <test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts_selector" value="advanced"/>
-    <param name="adv_opts_cond|test" value="true"/>
-    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
-       <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
-    </output>
-  </test>
-</xml>
-<xml name="manutest_MetaboliteAdductDecharger"/><xml name="manutest_IDMapper"/><xml name="manutest_ProteinQuantifier"/><xml name="manutest_PeakPickerIterative"/><xml name="manutest_FeatureLinkerUnlabeledQT"/><xml name="manutest_TICCalculator"/><xml name="manutest_IDFilter"/><xml name="manutest_IDPosteriorErrorProbability"/><xml name="manutest_FeatureFinderIdentification"/><xml name="manutest_XFDR"/><xml name="manutest_OpenSwathWorkflow"/><xml name="manutest_MassCalculator"/><xml name="manutest_IDFileConverter"/><xml name="manutest_MultiplexResolver"/><xml name="manutest_FeatureFinderSuperHirn"/><xml name="manutest_AssayGeneratorMetabo"/><xml name="manutest_MassTraceExtractor"/><xml name="manutest_SiriusAdapter"/><xml name="manutest_IDMerger"/><xml name="manutest_MSstatsConverter"/><xml name="manutest_FileMerger"/><xml name="manutest_Decharger"/><xml name="manutest_PTPredict"/><xml name="manutest_XTandemAdapter"/><xml name="manutest_FeatureFinderMetabo"/><xml name="manutest_CruxAdapter"/><xml name="manutest_OpenSwathConfidenceScoring"/><xml name="manutest_PrecursorIonSelector"/><xml name="manutest_ConsensusMapNormalizer"/><xml name="manutest_RTPredict"/><xml name="manutest_PercolatorAdapter"/><xml name="manutest_ProteinInference"/><xml name="manutest_OpenSwathDecoyGenerator"/><xml name="manutest_TextExporter"/><xml name="manutest_FeatureFinderCentroided"/><xml name="manutest_DecoyDatabase"/><xml name="manutest_SpectraFilterWindowMower"/><xml name="manutest_NoiseFilterGaussian"/><xml name="manutest_MaRaClusterAdapter"/><xml name="manutest_ConsensusID"/><xml name="manutest_FileFilter"/><xml name="manutest_InclusionExclusionListCreator"/><xml name="manutest_FeatureLinkerUnlabeledKD"/><xml name="manutest_NovorAdapter"/><xml name="manutest_OpenPepXL"/><xml name="manutest_SeedListGenerator"/><xml name="manutest_FalseDiscoveryRate"/><xml name="manutest_OpenPepXLLF"/><xml name="manutest_SpecLibSearcher"/><xml name="manutest_IDConflictResolver"/><xml name="manutest_MRMMapper"/><xml name="manutest_OMSSAAdapter"/><xml name="manutest_ExternalCalibration"/><xml name="manutest_PeakPickerHiRes"/><xml name="manutest_MascotAdapter"/><xml name="manutest_FeatureFinderMultiplex"/><xml name="manutest_MetaProSIP"/><xml name="manutest_FuzzyDiff"/><xml name="manutest_TargetedFileConverter"/><xml name="manutest_MapAlignerIdentification"/><xml name="manutest_IDRTCalibration"/><xml name="manutest_MRMTransitionGroupPicker"/><xml name="manutest_RTModel"/><xml name="manutest_OpenSwathAssayGenerator"/><xml name="manutest_IDSplitter"/><xml name="manutest_OpenSwathMzMLFileCacher"/><xml name="manutest_HighResPrecursorMassCorrector"/><xml name="manutest_OpenSwathChromatogramExtractor"/><xml name="manutest_OpenSwathAnalyzer"/><xml name="manutest_FeatureLinkerUnlabeled"/><xml name="manutest_CompNovoCID"/><xml name="manutest_DTAExtractor"/><xml name="manutest_FileInfo"/><xml name="manutest_MapAlignerSpectrum"/><xml name="manutest_IsobaricAnalyzer"/><xml name="manutest_LowMemPeakPickerHiRes"/><xml name="manutest_MyriMatchAdapter"/><xml name="manutest_InternalCalibration"/><xml name="manutest_TOFCalibration"/><xml name="manutest_MSGFPlusAdapter"/><xml name="manutest_PTModel"/><xml name="manutest_InspectAdapter"/><xml name="manutest_SpectraFilterSqrtMower"/><xml name="manutest_SimpleSearchEngine"/><xml name="manutest_PeakPickerWavelet"/><xml name="manutest_MapNormalizer"/><xml name="manutest_IDScoreSwitcher"/><xml name="manutest_FeatureLinkerLabeled"/><xml name="manutest_MapRTTransformer"/><xml name="manutest_RNPxlSearch"/><xml name="manutest_PrecursorMassCorrector"/><xml name="manutest_MapAlignerPoseClustering"/><xml name="manutest_MzTabExporter"/><xml name="manutest_BaselineFilter"/><xml name="manutest_FeatureFinderMRM"/><xml name="manutest_MascotAdapterOnline"/><xml name="manutest_DatabaseFilter"/><xml name="manutest_ProteinResolver"/><xml name="manutest_OpenSwathFeatureXMLToTSV"/><xml name="manutest_FidoAdapter"/><xml name="manutest_AccurateMassSearch"/><xml name="manutest_CompNovo"/><xml name="manutest_LowMemPeakPickerHiResRandomAccess"/><xml name="manutest_OpenSwathRTNormalizer"/><xml name="manutest_PeptideIndexer"/><xml name="manutest_CometAdapter"/><xml name="manutest_NoiseFilterSGolay"/><xml name="manutest_MSFraggerAdapter"/><xml name="manutest_SpectraSTSearchAdapter"/><xml name="manutest_SequestAdapter"/><xml name="manutest_FeatureFinder"/><xml name="manutest_LuciphorAdapter"/><xml name="manutest_GNPSExport"/><xml name="manutest_Epifany"/><xml name="manutest_NucleicAcidSearchEngine"/><xml name="manutest_QualityControl"/><xml name="manutest_FeatureFinderMetaboIdent"/><xml name="manutest_RNAMassCalculator"/><xml name="manutest_MapAlignerTreeGuided"/><xml name="manutest_IDMassAccuracy"/><xml name="manutest_ProteomicsLFQ"/><xml name="manutest_IDDecoyProbability"/><xml name="manutest_DigestorMotif"/><xml name="manutest_DatabaseSuitability"/><xml name="manutest_StaticModification"/></macros>
diff -r aa43ad3b2da6 -r aa8658367608 prepare_test_data_manual.sh
--- a/prepare_test_data_manual.sh	Fri Nov 06 19:59:16 2020 +0000
+++ b/prepare_test_data_manual.sh	Thu Dec 01 19:06:27 2022 +0000
@@ -86,10 +86,13 @@
 PhosphoScoring -in spectra.mzML -id MSGFPlusAdapter_1_out1.tmp -out PhosphoScoring.idxml > PhosphoScoring.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PhosphoScoring failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
-PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr
+# TODO PSMFeatureExtractor should have auto tests with 2.7 https://github.com/OpenMS/OpenMS/pull/5087 
+PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type idXML -out PSMFeatureExtractor.idxml > PSMFeatureExtractor_1.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
-PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr
+PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML XTandemAdapter_1_out.idXML -multiple_search_engines -skip_db_check -out_type mzid -out PSMFeatureExtractor.mzid > PSMFeatureExtractor_2.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_2 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
+PSMFeatureExtractor -test -in MSGFPlusAdapter_1_out.idXML -out_type idXML -out PSMFeatureExtractor_3.idXML > PSMFeatureExtractor_3.stdout 2> stderr
+if [[ "$?" -ne "0" ]]; then >&2 echo 'PSMFeatureExtractor_3 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
 
 QCCalculator -test -in OpenPepXL_input.mzML -out QCCalculator1.qcML > QCCalculator_1.stdout 2> stderr
 if [[ "$?" -ne "0" ]]; then >&2 echo 'QCCalculator_1 failed'; >&2 echo -e "stderr:\n$(cat stderr | sed 's/^/    /')"; fi
diff -r aa43ad3b2da6 -r aa8658367608 readme.md
--- a/readme.md	Fri Nov 06 19:59:16 2020 +0000
+++ b/readme.md	Thu Dec 01 19:06:27 2022 +0000
@@ -22,11 +22,14 @@
 
 Manual updates should only be done to
 
-- the `@GALAXY_VERSION@"` token in `macros.xml`
 - and the manually contributed tests in `macros_test.xml` (The goal is that all
   tools that do not have an automatically generated test are covered here)
 - the `hardcoded_params.json` files
 
+Wrapper versions are managed in `bump.json`. For tools listed in the file
+the wrapper version will be set accordingly and otherwise `0` is used. 
+For a major update of the tool version the bump file should be reset (to `{}`).
+
 In a few cases patches may be acceptable.
 
 Installation
@@ -71,10 +74,15 @@
 
 Preprocessing:
 
-- For each input / output data set parameter a directory is crated (named by
-  the parameter)
 - For input data set parameters the links to the actual location of the data
-  sets are created
+  sets are created, the link names are `element_identifier`.`EXT`, where `EXT`
+  is an extension that is known by OpenMS
+- In order to avoid name collisions for the created links each is placed in a
+  unique directory: `PARAM_NAME/DATASET_ID`, where `PARAM_NAME` is the name
+  of the parameter and `DATASET_ID` is the id of the Galaxy dataset 
+- the same happens for output parameters that are in 1:1 correspondence with
+  an input parameter
+
 
 Main:
 
diff -r aa43ad3b2da6 -r aa8658367608 test-data.sh
--- a/test-data.sh	Fri Nov 06 19:59:16 2020 +0000
+++ b/test-data.sh	Thu Dec 01 19:06:27 2022 +0000
@@ -1,22 +1,25 @@
 #!/usr/bin/env bash
 
-VERSION=2.6
-FILETYPES="filetypes.txt"
-CONDAPKG="https://anaconda.org/bioconda/openms/2.6.0/download/linux-64/openms-2.6.0-h4afb90d_0.tar.bz2"
+VERSION=2.8
+FILETYPES="aux/filetypes.txt"
+CONDAPKG="https://anaconda.org/bioconda/openms/2.8.0/download/linux-64/openms-2.8.0-h7ca0330_0.tar.bz2"
 
 # import the magic
 . ./generate-foo.sh
 
 # install conda
 if [ -z "$tmp" ]; then
-	tmp=$(mktemp -d)
-	created="yes"
+    tmp=$(mktemp -d)
+    created="yes"
 fi
 
 export OPENMSGIT="$tmp/OpenMS$VERSION.0-git"
 export OPENMSPKG="$tmp/OpenMS$VERSION-pkg/"
-export OPENMSENV="$tmp/OpenMS$VERSION-env"
-export CTDCONVERTER="$tmp/CTDConverter"
+export OPENMSENV="OpenMS$VERSION-env"
+
+if [ -z "$CTDCONVERTER" ]; then
+    export CTDCONVERTER="$tmp/CTDConverter"
+fi
 
 if [[ -z "$1" ]]; then
 	autotests="/dev/null"
@@ -25,11 +28,11 @@
 fi
 
 if type conda > /dev/null; then  
-	true
+    true
 else
-	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-	bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
-	source "$tmp/miniconda/bin/activate"
+    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
+    source "$tmp/miniconda/bin/activate"
 fi
 eval "$(conda shell.bash hook)"
 
@@ -42,24 +45,27 @@
 
 echo "Clone OpenMS $VERSION sources"
 if [[ ! -d $OPENMSGIT ]]; then
-	git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
-	cd $OPENMSGIT
-	git submodule init
-	git submodule update
-	cd -
+    # TODO >2.8 reenable original release branch .. also in else branch
+    # the plus branch contains commits from https://github.com/OpenMS/OpenMS/pull/5920 and https://github.com/OpenMS/OpenMS/pull/5917
+    # git clone -b release/$VERSION.0 https://github.com/OpenMS/OpenMS.git $OPENMSGIT
+    git clone -b release/$VERSION.0-plus https://github.com/bernt-matthias/OpenMS.git $OPENMSGIT
+    cd $OPENMSGIT
+    git submodule init
+    git submodule update
+    cd -
 else
-	cd $OPENMSGIT
-	git pull origin release/$VERSION.0
-	cd -
+    cd $OPENMSGIT
+    git pull origin release/$VERSION.0-plus
+    cd -
 fi
 
 echo "Create OpenMS $VERSION conda env"
 # TODO currently add lxml (needed by CTDConverter)
 # TODO for some reason a to recent openjdk is used
 if conda env list | grep "$OPENMSENV"; then
-	true
+    true
 else
-	conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -p $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION ctdopts=1.4 lxml
+    conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults -n $OPENMSENV openms=$VERSION openms-thirdparty=$VERSION omssa=2.1.9 ctdopts=1.5 lxml
 # chmod -R u-w $OPENMSENV 
 fi
 ###############################################################################
@@ -69,10 +75,10 @@
 echo "Download OpenMS $VERSION package $CONDAPKG"
 
 if [[ ! -d $OPENMSPKG ]]; then
-	mkdir $OPENMSPKG
-	wget -q -P $OPENMSPKG/ "$CONDAPKG"
-	tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
-	rm $OPENMSPKG/"$(basename $CONDAPKG)"
+    mkdir $OPENMSPKG
+    wget -q -P $OPENMSPKG/ "$CONDAPKG"
+    tar -xf $OPENMSPKG/"$(basename $CONDAPKG)" -C $OPENMSPKG/
+    rm $OPENMSPKG/"$(basename $CONDAPKG)"
 fi
 
 ###############################################################################
@@ -81,40 +87,46 @@
 ###############################################################################
 echo "Clone CTDConverter"
 if [[ ! -d $CTDCONVERTER ]]; then
-	#git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
-	git clone -b topic/cdata https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
+    #git clone https://github.com/WorkflowConversion/CTDConverter.git CTDConverter
+    git clone -b topic/fix-selects2 https://github.com/bernt-matthias/CTDConverter.git $CTDCONVERTER
 else
-	cd $CTDCONVERTER
-	git pull origin topic/cdata
-	cd -
+    cd $CTDCONVERTER
+    git pull origin topic/fix-selects2
+    cd -
 fi
+conda activate $OPENMSENV
+cd $CTDCONVERTER
+python -m pip install . --no-deps
+cd -
+conda deactivate
 
-###############################################################################
-## copy all the test data files to test-data
-## most of it (outputs) will be overwritten later, but its needed for
-## prepare_test_data
-###############################################################################
+
+# ###############################################################################
+# ## copy all the test data files to test-data
+# ## most of it (outputs) will be overwritten later, but its needed for
+# ## prepare_test_data
+# ###############################################################################
 echo "Get test data"
-find test-data -type f,l,d ! -name "*fa"  ! -name "*loc" -delete
+find test-data -type f,l,d ! -name "*fa" ! -name "*loc" ! -name "test-data" -delete
 
 cp $(find $OPENMSGIT/src/tests/topp/ -type f | grep -Ev "third_party_tests.cmake|CMakeLists.txt|check_ini") test-data/
 cp -r $OPENMSGIT/share/OpenMS/MAPPING/ test-data/
 cp -r $OPENMSGIT/share/OpenMS/CHEMISTRY test-data/
 cp -r $OPENMSGIT/share/OpenMS/examples/ test-data/
-if [[ ! -f test-data/MetaboliteSpectralDB.mzML ]]; then 
-	wget -nc https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
-	mv MetaboliteSpectralDB.mzML test-data/
+if [ ! -f test-data/MetaboliteSpectralDB.mzML ]; then 
+    wget -nc https://abibuilder.cs.uni-tuebingen.de/archive/openms/Tutorials/Data/latest/Example_Data/Metabolomics/databases/MetaboliteSpectralDB.mzML
+    mv MetaboliteSpectralDB.mzML test-data/
 fi
 ln -fs TOFCalibration_ref_masses test-data/TOFCalibration_ref_masses.txt
 ln -fs TOFCalibration_const test-data/TOFCalibration_const.csv
 
 if [ ! -d test-data/pepnovo_models/ ]; then
-	mkdir -p /tmp/pepnovo
-	wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
-	unzip PepNovo.20120423.zip -d /tmp/pepnovo/
-	mv /tmp/pepnovo/Models test-data/pepnovo_models/
-	rm PepNovo.20120423.zip
-	rm -rf /tmp/pepnovo
+    mkdir -p /tmp/pepnovo
+    wget -nc http://proteomics.ucsd.edu/Software/PepNovo/PepNovo.20120423.zip
+    unzip PepNovo.20120423.zip -d /tmp/pepnovo/
+    mv /tmp/pepnovo/Models test-data/pepnovo_models/
+    rm PepNovo.20120423.zip
+    rm -rf /tmp/pepnovo
 fi
 ###############################################################################
 ## generate ctd files using the binaries in the conda package 
@@ -124,17 +136,13 @@
 rm -rf ctd
 mkdir -p ctd
 
-# TODO because of https://github.com/OpenMS/OpenMS/issues/4641
-# this needs to be done from within test-data
-cd test-data
 for i in $OPENMSPKG/bin/*
 do
-	b=$(basename $i)
-	echo $b
-	$b -write_ctd ../ctd/
-	sed -i -e 's/²/^2/' ../ctd/$b.ctd
+    b=$(basename $i)
+    echo $b
+    $b -write_ctd ctd/
+    sed -i -e 's/²/^2/' ctd/$b.ctd
 done
-cd -
 ###############################################################################
 ## fix ini files: OpenMS test data contains ini files with outdated ini files.
 ## e.g. variables might be in different nodes, outdated variables present, new
@@ -146,17 +154,17 @@
 echo "Update test INI files"
 for ini in test-data/*ini
 do
-	tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
-	bin=$(which $tool)
-	if [[ -z $bin ]]; then
+    tool=$(cat $ini | grep 'NODE name="' | head -n 1 | sed 's/.*name="\([^"]\+\)".*/\1/')
+    bin=$(which $tool)
+    if [[ -z $bin ]]; then
           >&2 echo "missing binary to convert $ini"
-		  continue
-	fi
-	cp $ini $ini.backup
-	$bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
-	if [[ "$?" -ne "0" ]]; then
-		>&2 echo "could not convert $ini"
-	fi
+          continue
+    fi
+    cp $ini $ini.backup
+    $bin -ini $ini -write_ini $ini > $ini.stdout 2> $ini.stderr
+    if [[ "$?" -ne "0" ]]; then
+        >&2 echo "could not convert $ini"
+    fi
 done
 
 ###############################################################################
@@ -185,17 +193,17 @@
 
 prepare_test_data >> prepare_test_data.sh #tmp_test_data.sh
 
-# prepare_test_data > tmp_test_data.sh
-# # remove calls not needed for the tools listed in any .list file
-# echo LIST $LIST
-# if [ ! -z "$LIST" ]; then
-# 	REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
-# else
-# 	REX=".*"
-# fi
-# echo REX $REX
-# cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
-# rm tmp_test_data.sh
+## prepare_test_data > tmp_test_data.sh
+## # remove calls not needed for the tools listed in any .list file
+## echo LIST $LIST
+## if [ ! -z "$LIST" ]; then
+##     REX=$(echo $LIST | sed 's/ /\n/g' | sed 's@.*/\([^/]\+\).xml$@\1@' | tr '\n' '|' | sed 's/|$//')
+## else
+##     REX=".*"
+## fi
+## echo REX $REX
+## cat tmp_test_data.sh | egrep "($REX)" >> prepare_test_data.sh
+## rm tmp_test_data.sh
 
 echo "Execute test shell script"
 chmod u+x prepare_test_data.sh
@@ -204,14 +212,13 @@
 cd - || exit
 
 
-###############################################################################
-## create/update test data for the manually generated tests
-## - run convert once with the manual tests only and 
-## - update test-data (needs to run 2x)
-###############################################################################
+# ###############################################################################
+# ## create/update test data for the manually generated tests
+# ## - run convert once with the manual tests only and 
+# ## - update test-data (needs to run 2x)
+# ###############################################################################
 echo "Execute test shell script for manually curated tests"
 chmod u+x prepare_test_data_manual.sh
-
 cd ./test-data || exit
 ../prepare_test_data_manual.sh
 cd - || exit
@@ -220,22 +227,28 @@
 ###############################################################################
 ## auto generate tests
 ###############################################################################
+
 echo "Write test macros to $autotests"
 echo "<macros>" > "$autotests"
-for i in $(ls *xml |grep -v macros)
+
+for i in $(ls ctd/*ctd)
 do
-	b=$(basename "$i" .xml)
-	get_tests2 "$b" >> "$autotests"
+    b=$(basename "$i" .ctd)
+    get_tests2 "$b" >> "$autotests"
 done
 echo "</macros>" >> "$autotests"
 
-echo "Create test data links"
-link_tmp_files
+# echo "Create test data links"
+# Breaks DecoyDatabase
+# link_tmp_files
 
 # tests for tools using output_prefix parameters can not be auto generated
 # hence we output the tests for manual curation in macros_test.xml
 # and remove them from the autotests
-# -> OpenSwathFileSplitter IDRipper MzMLSplitter
+# -> OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator
+# TODO reevaluate in >2.8 
+# - https://github.com/OpenMS/OpenMS/pull/5873
+# - https://github.com/OpenMS/OpenMS/pull/5912
 #
 # Furthermore we remove tests for tools without binaries in conda
 # -> MSFragger MaRaClusterAdapter NovorAdapter 
@@ -243,23 +256,23 @@
 # not able to specify composite test data  
 # -> SpectraSTSearchAdapter 
 if [[ ! -z "$1" ]]; then
-	echo "" > macros_discarded_auto.xml
-	for i in OpenSwathFileSplitter IDRipper MzMLSplitter MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
-	do
-		echo "<xml name=\"manutest_$i\">" >>  macros_discarded_auto.xml
-		xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >>  macros_discarded_auto.xml
-		echo "</xml>"  >>  macros_discarded_auto.xml
-		xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
-		mv tmp macros_autotest.xml
-	done
-	>&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
+    echo "" > macros_discarded_auto.xml
+    for i in OpenSwathFileSplitter IDRipper MzMLSplitter SeedListGenerator MSFraggerAdapter MaRaClusterAdapter NovorAdapter SpectraSTSearchAdapter
+    do
+        echo "<xml name=\"manutest_$i\">" >>  macros_discarded_auto.xml
+        xmlstarlet sel -t -c "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml >>  macros_discarded_auto.xml
+        echo "</xml>"  >>  macros_discarded_auto.xml
+        xmlstarlet ed -d "/macros/xml[@name='autotest_$i']/test" macros_autotest.xml > tmp
+        mv tmp macros_autotest.xml
+    done
+    >&2 echo "discarded autogenerated macros for curation in macros_discarded_auto.xml"
 fi
 conda deactivate
 
 ## remove broken symlinks in test-data
 find test-data/ -xtype l -delete
 
-# if [ ! -z "$created" ]; then
-# 	echo "Removing temporary directory"
-# 	rm -rf "$tmp"
-# fi
+if [ ! -z "$created" ]; then
+    echo "Removing temporary directory"
+    rm -rf "$tmp"
+fi
diff -r aa43ad3b2da6 -r aa8658367608 test-data/pepnovo_models.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pepnovo_models.loc	Thu Dec 01 19:06:27 2022 +0000
@@ -0,0 +1,13 @@
+#name	value	path
+default_models	CID_IT_TRYP	${__HERE__}/pepnovo_models/
+default_models	LTQ_COMP	${__HERE__}/pepnovo_models/
+default_models	DBC4_PEAK	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_TAG5	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_TAG6	${__HERE__}/pepnovo_models/
+default_models	ITDNV_PEAK	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_SCORE	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_TAG3	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_DNVPART	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_TAG4	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_DB	${__HERE__}/pepnovo_models/
+default_models	CID_IT_TRYP_CSP	${__HERE__}/pepnovo_models/
diff -r aa43ad3b2da6 -r aa8658367608 test-data/random.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random.fa	Thu Dec 01 19:06:27 2022 +0000
@@ -0,0 +1,18 @@
+>RND24402 Randomly generated sequence, created by ExPASy tool RandSeq, using average amino acid composition
+LALLTDKYSVTKSIKGYAGQQQKCTDDEGLAEDSAAMSLVPIRAAWTISVSVDLFYLGIV
+TNVTKDSVEHLVGIPLVTHEFMASRCEMRGQVVSATFGSWQKAESKAYRIPLKATPLDEF
+VESAVYLFGGSSNEYECVLIGNSHPVLIFLDIDAVPGARKPRTGFFMAEGFHSKGETRAL
+VGKSPPLGEYRKGAFHFTFPIKEAIRLGPPKKRIMGYRDALEGGLNHYVQTQVLVLLPMI
+QVARRWENGLGLLVGKFLKLPTHPLDLNQVTLCWSEAVTEDNKRFLLTIKTSAQGKSAPT
+SHINYVPQHNSMELMAINGSPFAAQHKSNDEIESMRDLSKLYADAETLESHGERGVRHQA
+TETKISKVTNLRRKLPQLLDLNVVDNACNWESVGAHVLEYVLVNLYLKELQEPKVELQPR
+LNETTMKAGASSLGVESGASAHSFYKGGVSEAKLRFRHVATPAAARIWWCVVMFRINRRY
+DGITYNSVGEQLSGVHEYVRAAQLFGLTTGKNLRSTGIVIIKLSTAIDLECLVQAKPKEA
+YVLANDYIGAKPHPARLETGPALVLFIVETINNDTLNAAILITALGGKFLNVRPDLLFGV
+QALFGCVRMFRHADCTIGREKFVQTEISHKAKFLYEINEFFLERILQFEEAKSPVGAPAY
+DIPIGRGLVMDSSTDLWNIYVVELISGQEKRTGIDPDTPMGTSHNLYMTDARLDERDQRS
+FLNSEFVKPSKLANGSEWADPYVEPDKTEVIAFFPATLIVIMADGSALNGQVCIQPAKDN
+SKMADDLATVHIGQDRPCDWGISASHEYDEVNRPARINGVMMQQLMAEDNQGPGASPRDQ
+MGDADDLKEIKWNKYVIDNEIIGRERGISAERVKIFLGDTLTARGLLDSPPGQTKVFDLR
+PRQSDKNQSGMFKRDQNAMYFPLEYDRIGAQTDTGSLYSTLITKFASISIDLVKLSMPRE
+KQIDEERLHSEFIENQKRSALPAVQKNLACISCVEACRGT
diff -r aa43ad3b2da6 -r aa8658367608 test-data/random_RNA.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/random_RNA.fa	Thu Dec 01 19:06:27 2022 +0000
@@ -0,0 +1,2 @@
+> random RNA
+GUGUUACUGCCACGAAACAAAAUGUUCAAGACACCGGGCGCCAUCUGUAUAUUACUCGCCAAUCAGACGGUCUGCAACGCUACAGACAUGGAGCUCAGCGCUGACGAUGUCGCCGGACCAAGUACGAUCACUUUGCUCGUGCAAAUGUUCGUCCGCAUUGGGCACUAUAACUCGAAUUGUCGAAUCCGGGUGGCGAGCCGCCACUUAUAGGAUAAAUAUUCAAACUAACAUUAUGGCGCCAAAUCUGCAAUCUCUACUUUAGACAUUAUAUACCCACAUUUACAAUUAGAGUUAUUAUUAGUUAACGUGUGCCAGAGCAGGGAUGGCUCUUGUCAGCCAUAGUUGUGUGAACGGGCUGUAUUUCCUUCCUAAUUAUAGAGCGGCACCGGAAAGCAAUGCACGAUCCACGAGGGCACUUCACAUGGUCACAAACAGUCAUUCUGGUACCCUGAUUCGUUCCCGAAAGGGAAGUAUAUACACGGCCCCCGUGUAUAUCGCCAGUCACACGGCAGGAGCGAGAGUUCGUUUGUAUACAUGCCCAGGAGCCUUCUCUAACUUUUGAAGCUGUGCAACUUUGUUGGCGCGUCACCACUAAGUCAGCUUAAUAGACAGCAGAUGGGAGAAUUUACCAUUUCAUUUUGUCCGAGCUGAUACCGGUAGGUCAUCUCUAAUCACCCGUUAUCCUCUCGUAAUAUAAUCGCUACUAAGGUAUGAAGGUGUCUGCGAAAGGUAACGUAAAUCAUUCUCGGCUCCUUGCAAAGUACGACUAGGAUCCAUCGUACACAUCCGGACGAAGAUGUAAAAUUGACGCCCCUGUAGGCCGUGAGACAGACGUGAGCCAAACCAUCUGCUCUACUUCUGGAGGCCUUGAAUAGUGGCGCGUUGUGUAAUCUUAAGAGAGAUUUUACUUGGAAUUACAGCCUACUUUGACCAGUAGCGCAUUGUGAACAAAUAUUCCCGUACGCGUCCAAUUGCAGCAAAACGUGGGCCUGUGUCCAGU
diff -r aa43ad3b2da6 -r aa8658367608 tools_blacklist.txt
--- a/tools_blacklist.txt	Fri Nov 06 19:59:16 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-# seems not possible for 2.5 https://github.com/OpenMS/OpenMS/issues/4426
-# DigestorMotif
-
-# deprecated https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_IDDecoyProbability.html
-# https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/a16242.html
-IDDecoyProbability
-
-# personal communication with author V. Bafna: 
-# "InsPect is no longer maintained as there are many better tools including MS-GF+"
-InspectAdapter
-
-# licence? see https://github.com/bioconda/bioconda-recipes/issues/18953
-#MSFraggerAdapter
-
-# https://github.com/OpenMS/OpenMS/issues/4550#issuecomment-594065727
-ProteomicsLFQ
-
-# https://github.com/OpenMS/OpenMS/issues/4401
-InclusionExclusionListCreator
-RTPredict
-PTPredict