--- a/MSstatsConverter.xml	Fri Nov 06 19:41:20 2020 +0000
+++ b/MSstatsConverter.xml	Thu Dec 01 19:13:23 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: [Utilities]-->
-<tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="MSstatsConverter" name="MSstatsConverter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Converter to input for MSstats</description>
   <macros>
     <token name="@EXECUTABLE@">MSstatsConverter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -21,12 +19,15 @@
 mkdir in_design &&
 ln -s '$in_design' 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)' &&
 mkdir out &&
-#if $adv_opts_cond.adv_opts_selector=='advanced':
-  #if $adv_opts_cond.reannotate_filenames:
-    mkdir adv_opts_cond.reannotate_filenames &&
-    ${ ' '.join(["ln -s '%s' 'adv_opts_cond.reannotate_filenames/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _]) }
+  #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
+    mkdir adv_opts.reannotate_filenames_cond.reannotate_filenames &&
+    #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
+    mkdir ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s'" % (i) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])} && 
+    ${' '.join(["ln -s '%s' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
+    #else
+    ln -s '$adv_opts.reannotate_filenames_cond.reannotate_filenames' 'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)' &&
+    #end if
   #end if
-#end if
 
 ## Main program call
 
@@ -40,12 +41,14 @@
 'in_design/${re.sub("[^\w\-_]", "_", $in_design.element_identifier)}.$gxy2omsext($in_design.ext)'
 -out
 'out/output.${gxy2omsext("csv")}'
-#if $adv_opts_cond.adv_opts_selector=='advanced':
-  #if $adv_opts_cond.reannotate_filenames:
+  #if $adv_opts.reannotate_filenames_cond.reannotate_filenames:
     -reannotate_filenames
-    ${' '.join(["'adv_opts_cond.reannotate_filenames/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $adv_opts_cond.reannotate_filenames if _])}
+    #if $adv_opts.reannotate_filenames_cond.reannotate_filenames_select == "no"
+    ${' '.join(["'adv_opts.reannotate_filenames_cond.reannotate_filenames/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($adv_opts.reannotate_filenames_cond.reannotate_filenames) if f])}
+    #else
+    'adv_opts.reannotate_filenames_cond.reannotate_filenames/${re.sub("[^\w\-_]", "_", $adv_opts.reannotate_filenames_cond.reannotate_filenames.element_identifier)}.$gxy2omsext($adv_opts.reannotate_filenames_cond.reannotate_filenames.ext)'
+    #end if
   #end if
-#end if
 
 ## Postprocessing
 && mv 'out/output.${gxy2omsext("csv")}' '$out'
@@ -57,36 +60,47 @@
     <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" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
-    <param name="in_design" argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
-    <param name="method" argument="-method" display="radio" type="select" optional="false" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
+    <param argument="-in" type="data" format="consensusxml" optional="false" label="Input consensusXML with peptide intensities" help=" select consensusxml data sets(s)"/>
+    <param argument="-in_design" type="data" format="tabular" optional="false" label="Experimental Design file" help=" select tabular data sets(s)"/>
+    <param argument="-method" type="select" optional="true" label="Method used in the experiment(label free [LFQ], isobaric labeling [ISO]))" help="">
       <option value="LFQ" selected="true">LFQ</option>
       <option value="ISO">ISO</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="method"/>
+    </param>
+    <param argument="-msstats_bioreplicate" type="text" optional="true" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
+      <expand macro="list_string_san" name="msstats_bioreplicate"/>
     </param>
-    <param name="msstats_bioreplicate" argument="-msstats_bioreplicate" type="text" optional="true" value="MSstats_BioReplicate" label="Which column in the condition table should be used for MSstats 'BioReplicate'" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-msstats_condition" type="text" optional="true" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
+      <expand macro="list_string_san" name="msstats_condition"/>
     </param>
-    <param name="msstats_condition" argument="-msstats_condition" type="text" optional="true" value="MSstats_Condition" label="Which column in the condition table should be used for MSstats 'Condition'" help="">
-      <expand macro="list_string_san"/>
+    <param argument="-msstats_mixture" type="text" optional="true" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
+      <expand macro="list_string_san" name="msstats_mixture"/>
     </param>
-    <param name="msstats_mixture" argument="-msstats_mixture" type="text" optional="true" value="MSstats_Mixture" label="Which column in the condition table should be used for MSstats 'Mixture'" help="">
-      <expand macro="list_string_san"/>
-    </param>
-    <param name="labeled_reference_peptides" argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
+    <param argument="-labeled_reference_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, IsotopeLabelType is 'H', else 'L'" help=""/>
     <expand macro="adv_opts_macro">
-      <param name="reannotate_filenames" argument="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
-      <param name="retention_time_summarization_method" argument="-retention_time_summarization_method" type="select" optional="false" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
+      <conditional name="reannotate_filenames_cond">
+        <param name="reannotate_filenames_select" type="select" label="Run tool in batch mode for -reannotate_filenames">
+          <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="-reannotate_filenames" type="data" format="mzml" multiple="true" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+        </when>
+        <when value="yes">
+          <param argument="-reannotate_filenames" type="data" format="mzml" multiple="false" optional="true" label="Overwrite MS file names in consensusXML" help=" select mzml data sets(s)"/>
+        </when>
+      </conditional>
+      <param argument="-retention_time_summarization_method" type="select" optional="true" label="How indistinguishable peptidoforms at different retention times should be treated" help="This is usually necessary for LFQ experiments and therefore defaults to 'max'. In case of TMT/iTRAQ, MSstatsTMT does the aggregation itself later and the parameter always resets to manual (i.e. is unused)">
         <option value="manual">manual</option>
         <option value="max" selected="true">max</option>
         <option value="min">min</option>
         <option value="mean">mean</option>
         <option value="sum">sum</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="retention_time_summarization_method"/>
       </param>
-      <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">
@@ -99,13 +113,76 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_MSstatsConverter"/>
-    <expand macro="manutest_MSstatsConverter"/>
+  <tests><!-- TOPP_MSstatsConverter_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="retention_time_summarization_method" value="max"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <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_frac="0.7" 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>
+    <!-- TOPP_MSstatsConverter_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="retention_time_summarization_method" value="manual"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <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_frac="0.7" 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>
+    <!-- TOPP_MSstatsConverter_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="retention_time_summarization_method" value="manual"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <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_frac="0.7" 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>
   </tests>
   <help><![CDATA[Converter to input for MSstats
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSstatsConverter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MSstatsConverter.html]]></help>
   <expand macro="references"/>
 </tool>