--- a/FeatureLinkerUnlabeled.xml	Fri May 17 09:53:15 2019 -0400
+++ b/FeatureLinkerUnlabeled.xml	Wed Sep 09 12:49:46 2020 +0000
@@ -1,124 +1,110 @@
 <?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="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.3.0">
+<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Groups corresponding features from multiple maps.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[FeatureLinkerUnlabeled
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
--in
-  #for token in $param_in:
-    $token
-  #end for
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_design:
-  -design $param_design
-#end if
-#if $param_keep_subelements:
-  -keep_subelements
-#end if
-#if $param_algorithm_second_nearest_gap:
-  -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
-#end if
-#if $param_algorithm_use_identifications:
-  -algorithm:use_identifications
+## Preprocessing
+mkdir in &&
+${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir out &&
+#if $design:
+  mkdir design &&
+  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
-#if $param_algorithm_ignore_charge:
-  -algorithm:ignore_charge
-#end if
-#if $param_algorithm_distance_RT_max_difference:
-  -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
-#end if
-#if $param_algorithm_distance_MZ_max_difference:
-  -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
-#end if
-#if $param_algorithm_distance_MZ_unit:
-  -algorithm:distance_MZ:unit
-  #if " " in str($param_algorithm_distance_MZ_unit):
-    "$param_algorithm_distance_MZ_unit"
-  #else
-    $param_algorithm_distance_MZ_unit
-  #end if
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-    #if $adv_opts.param_algorithm_distance_RT_exponent:
-  -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
-#end if
-    #if $adv_opts.param_algorithm_distance_RT_weight:
-  -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__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 $in if _])}
+-out
+'out/output.${gxy2omsext("consensusxml")}'
+#if $design:
+  -design
+  'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
 #end if
-    #if $adv_opts.param_algorithm_distance_MZ_exponent:
-  -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
-#end if
-    #if $adv_opts.param_algorithm_distance_MZ_weight:
-  -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
-#end if
-    #if $adv_opts.param_algorithm_distance_intensity_exponent:
-  -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
-#end if
-    #if $adv_opts.param_algorithm_distance_intensity_weight:
-  -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
-#end if
-    #if $adv_opts.param_algorithm_distance_intensity_log_transform:
-  -algorithm:distance_intensity:log_transform
-  #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform):
-    "$adv_opts.param_algorithm_distance_intensity_log_transform"
-  #else
-    $adv_opts.param_algorithm_distance_intensity_log_transform
-  #end if
-#end if
-#end if
-]]></command>
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <inputs>
-    <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
-    <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/>
-    <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
-    <param name="param_algorithm_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help="(-second_nearest_gap) "/>
-    <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help="(-use_identifications) "/>
-    <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
-    <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
-    <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
-    <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
-      <option value="Da" selected="true">Da</option>
-      <option value="ppm">ppm</option>
-    </param>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
-      <param name="param_algorithm_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
-      <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
-      <param name="param_algorithm_distance_MZ_exponent" type="float" min="0.0" optional="True" 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="(-exponent) "/>
-      <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
-      <param name="param_algorithm_distance_intensity_exponent" type="float" min="0.0" optional="True" 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="(-exponent) "/>
-      <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
-      <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) 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>
+    <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=""/>
+    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
+      <param name="second_nearest_gap" argument="-algorithm:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/>
+      <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 (features without ID's always match; only the best hit per peptide identification is considered)" help=""/>
+      <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">
+        <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/>
+        <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/>
+        <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/>
+      </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="">
+          <option value="Da" selected="true">Da</option>
+          <option value="ppm">ppm</option>
+          <expand macro="list_string_san"/>
+        </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=""/>
+      </section>
+      <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))">
+          <option value="enabled">enabled</option>
+          <option value="disabled" selected="true">disabled</option>
+          <expand macro="list_string_san"/>
+        </param>
+      </section>
+    </section>
+    <expand macro="adv_opts_macro">
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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>
     </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_out" format="consensusxml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Groups corresponding features from multiple maps.
+  <tests>
+    <expand macro="autotest_FeatureLinkerUnlabeled"/>
+    <expand macro="manutest_FeatureLinkerUnlabeled"/>
+  </tests>
+  <help><![CDATA[Groups corresponding features from multiple maps.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureLinkerUnlabeled.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_FeatureLinkerUnlabeled.html]]></help>
+  <expand macro="references"/>
 </tool>