--- a/OpenSwathAssayGenerator.xml	Fri Nov 06 20:41:52 2020 +0000
+++ b/OpenSwathAssayGenerator.xml	Thu Dec 01 19:07:50 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: [Targeted Experiments]-->
-<tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="OpenSwathAssayGenerator" name="OpenSwathAssayGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Generates assays according to different models for a specific TraML</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathAssayGenerator</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -57,41 +55,41 @@
     <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="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
-    <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file" help=" select mrm,pqp,tabular,traml data sets(s)"/>
+    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
       <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
       <option value="tsv">tabular (tsv)</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param name="min_transitions" argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/>
-    <param name="max_transitions" argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/>
-    <param name="allowed_fragment_types" argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-min_transitions" type="integer" optional="true" value="6" label="minimal number of transitions" help=""/>
+    <param argument="-max_transitions" type="integer" optional="true" value="6" label="maximal number of transitions" help=""/>
+    <param argument="-allowed_fragment_types" type="text" optional="true" value="b,y" label="allowed fragment types" help="">
+      <expand macro="list_string_san" name="allowed_fragment_types"/>
     </param>
-    <param name="allowed_fragment_charges" argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-allowed_fragment_charges" type="text" optional="true" value="1,2,3,4" label="allowed fragment charge states" help="">
+      <expand macro="list_string_san" name="allowed_fragment_charges"/>
     </param>
-    <param name="enable_detection_specific_losses" argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
-    <param name="enable_detection_unspecific_losses" argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
-    <param name="precursor_mz_threshold" argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
-    <param name="precursor_lower_mz_limit" argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/>
-    <param name="precursor_upper_mz_limit" argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
-    <param name="product_mz_threshold" argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
-    <param name="product_lower_mz_limit" argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/>
-    <param name="product_upper_mz_limit" argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
-    <param name="swath_windows_file" argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
-    <param name="unimod_file" argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
-    <param name="enable_ipf" argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
+    <param argument="-enable_detection_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if specific neutral losses for detection fragment ions should be allowed" help=""/>
+    <param argument="-enable_detection_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for detection fragment ions should be allowed" help=""/>
+    <param argument="-precursor_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for precursor ion selection" help=""/>
+    <param argument="-precursor_lower_mz_limit" type="float" optional="true" value="400.0" label="lower MZ limit for precursor ions" help=""/>
+    <param argument="-precursor_upper_mz_limit" type="float" optional="true" value="1200.0" label="upper MZ limit for precursor ions" help=""/>
+    <param argument="-product_mz_threshold" type="float" optional="true" value="0.025" label="MZ threshold in Thomson for fragment ion annotation" help=""/>
+    <param argument="-product_lower_mz_limit" type="float" optional="true" value="350.0" label="lower MZ limit for fragment ions" help=""/>
+    <param argument="-product_upper_mz_limit" type="float" optional="true" value="2000.0" label="upper MZ limit for fragment ions" help=""/>
+    <param argument="-swath_windows_file" type="data" format="txt" optional="true" label="Tab separated file containing the SWATH windows for exclusion of fragment ions falling into the precursor isolation window: lower_offset upper_offset \newline 400 425 \newline" help="Note that the first line is a header and will be skipped select txt data sets(s)"/>
+    <param argument="-unimod_file" type="data" format="xml" optional="true" label="(Modified) Unimod XML file (http://www.unimod.org/xml/unimod.xml) describing residue modifiability" help=" select xml data sets(s)"/>
+    <param argument="-enable_ipf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions should be generated for IPF" help="Note: Requires setting 'unimod_file'"/>
     <expand macro="adv_opts_macro">
-      <param name="max_num_alternative_localizations" argument="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
-      <param name="disable_identification_ms2_precursors" argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
-      <param name="disable_identification_specific_losses" argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
-      <param name="enable_identification_unspecific_losses" argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
-      <param name="enable_swath_specifity" argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
-      <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="-max_num_alternative_localizations" type="integer" optional="true" value="10000" label="IPF: maximum number of site-localization permutations" help=""/>
+      <param argument="-disable_identification_ms2_precursors" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if MS2-level precursor ions for identification should not be allowed for extraction of the precursor signal from the fragment ion data (MS2-level)" help=""/>
+      <param argument="-disable_identification_specific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if specific neutral losses for identification fragment ions should not be allowed" help=""/>
+      <param argument="-enable_identification_unspecific_losses" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) for identification fragment ions should be allowed" help=""/>
+      <param argument="-enable_swath_specifity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="IPF: set this flag if identification transitions without precursor specificity" help="(i.e. across whole precursor isolation window instead of precursor MZ) should be generated"/>
+      <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">
@@ -99,9 +97,8 @@
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out">
+    <data name="out" label="${tool.name} on ${on_string}: out" format="traml">
       <change_format>
-        <when input="out_type" value="TraML" format="traml"/>
         <when input="out_type" value="pqp" format="pqp"/>
         <when input="out_type" value="tsv" format="tabular"/>
       </change_format>
@@ -110,13 +107,114 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_OpenSwathAssayGenerator"/>
-    <expand macro="manutest_OpenSwathAssayGenerator"/>
+  <tests><!-- TOPP_OpenSwathAssayGenerator_test_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <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"/>
+      </section>
+      <param name="in" value="OpenSwathAssayGenerator_input.TraML"/>
+      <output name="out" file="OpenSwathAssayGenerator_output.TraML" compare="sim_size" delta_frac="0.7" 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>
+    <!-- TOPP_OpenSwathAssayGenerator_test_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <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"/>
+      </section>
+      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
+      <output name="out" file="OpenSwathAssayGenerator_output_2.TraML" compare="sim_size" delta_frac="0.7" 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>
+    <!-- TOPP_OpenSwathAssayGenerator_test_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <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"/>
+      </section>
+      <param name="in" value="OpenSwathAssayGenerator_input_2.TraML"/>
+      <output name="out" file="OpenSwathAssayGenerator_output_3.TraML" compare="sim_size" delta_frac="0.7" 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>
   </tests>
   <help><![CDATA[Generates assays according to different models for a specific TraML
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathAssayGenerator.html]]></help>
   <expand macro="references"/>
 </tool>