--- a/TargetedFileConverter.xml	Wed May 15 07:01:16 2019 -0400
+++ b/TargetedFileConverter.xml	Thu Aug 27 23:29:25 2020 +0000
@@ -1,78 +1,93 @@
 <?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="TargetedFileConverter" name="TargetedFileConverter" version="2.3.0">
+<tool id="TargetedFileConverter" name="TargetedFileConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description>
   <macros>
     <token name="@EXECUTABLE@">TargetedFileConverter</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[TargetedFileConverter
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+
+## Main program call
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_out_type:
-  -out_type
-  #if " " in str($param_out_type):
-    "$param_out_type"
-  #else
-    $param_out_type
-  #end if
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_legacy_traml_id:
-  -legacy_traml_id
-#end if
-    #if $adv_opts.param_force:
-  -force
-#end if
-    #if $adv_opts.param_algorithm_retentionTimeInterpretation:
-  -algorithm:retentionTimeInterpretation
-  #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation):
-    "$adv_opts.param_algorithm_retentionTimeInterpretation"
-  #else
-    $adv_opts.param_algorithm_retentionTimeInterpretation
-  #end if
-#end if
-    #if $adv_opts.param_algorithm_override_group_label_check:
-  -algorithm:override_group_label_check
-#end if
-    #if $adv_opts.param_algorithm_force_invalid_mods:
-  -algorithm:force_invalid_mods
-#end if
-#end if
-]]></command>
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${out_type}'
+
+## Postprocessing
+&& mv 'out/output.${out_type}' '$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="tabular,mrm,pqp,traml" optional="False" label="Input file to convert" help="(-in) &lt;br&gt; See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file"/>
-    <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
-      <option value="tsv">tsv</option>
+    <param name="in" argument="-in" type="data" format="mrm,pqp,tabular,traml" optional="false" label="Input file to convert" help="See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file 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="Note: that not all conversion paths work or make sense">
+      <option value="TraML">traml</option>
       <option value="pqp">pqp</option>
-      <option value="TraML">TraML</option>
+      <option value="tsv">tabular (tsv)</option>
+      <expand macro="list_string_san"/>
     </param>
-    <expand macro="advanced_options">
-      <param name="param_legacy_traml_id" display="radio" type="boolean" truevalue="-legacy_traml_id" falsevalue="" checked="false" optional="True" label="PQP to TraML: Should legacy TraML IDs be used?" help="(-legacy_traml_id) "/>
-      <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_retentionTimeInterpretation" display="radio" type="select" optional="False" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) ">
+    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
+      <param name="retentionTimeInterpretation" argument="-algorithm:retentionTimeInterpretation" display="radio" type="select" optional="false" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="">
         <option value="iRT" selected="true">iRT</option>
         <option value="seconds">seconds</option>
         <option value="minutes">minutes</option>
+        <expand macro="list_string_san"/>
       </param>
-      <param name="param_algorithm_override_group_label_check" display="radio" type="boolean" truevalue="-algorithm:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
-      <param name="param_algorithm_force_invalid_mods" display="radio" type="boolean" truevalue="-algorithm:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/>
+      <param name="override_group_label_check" argument="-algorithm:override_group_label_check" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="Only turn this off if you know what you are doing"/>
+      <param name="force_invalid_mods" argument="-algorithm:force_invalid_mods" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help=""/>
+    </section>
+    <expand macro="adv_opts_macro">
+      <param name="legacy_traml_id" argument="-legacy_traml_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="PQP to TraML: Should legacy TraML IDs be used?" help=""/>
+      <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" metadata_source="param_in" format="input"/>
+    <data name="out" label="${tool.name} on ${on_string}: out">
+      <change_format>
+        <when input="out_type" value="TraML" format="traml"/>
+        <when input="out_type" value="pqp" format="pqp"/>
+        <when input="out_type" value="tsv" format="tabular"/>
+      </change_format>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Converts different transition files for targeted proteomics / metabolomics analysis.
+  <tests>
+    <expand macro="autotest_TargetedFileConverter"/>
+    <expand macro="manutest_TargetedFileConverter"/>
+  </tests>
+  <help><![CDATA[Converts different transition files for targeted proteomics / metabolomics analysis.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_TargetedFileConverter.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_TargetedFileConverter.html]]></help>
+  <expand macro="references"/>
 </tool>