--- a/OpenSwathFeatureXMLToTSV.xml	Thu Dec 01 19:21:34 2022 +0000
+++ b/OpenSwathFeatureXMLToTSV.xml	Fri Jun 14 21:29:01 2024 +0000
@@ -1,8 +1,7 @@
-<?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]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Converts a featureXML to a mProphet tsv.</description>
+  <description>Converts a featureXML to a mProphet tsv</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
     <import>macros.xml</import>
@@ -17,12 +16,12 @@
 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])}
+${' '.join(["cp '%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($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -58,20 +57,20 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml" multiple="true" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="featurexml" multiple="false" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
+        <param argument="-in" type="data" format="featurexml" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-tr" type="data" format="traml" optional="false" label="TraML transition file" help=" select traml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" label="TraML transition file" help=" select traml data sets(s)"/>
     <param argument="-short_format" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write short (one peptide per line) or long format (one transition per line)" help=""/>
     <param argument="-best_scoring_peptide" type="text" optional="true" value="" label="If only the best scoring feature per peptide should be printed, give the variable name" help="">
       <expand macro="list_string_san" name="best_scoring_peptide"/>
     </param>
     <expand macro="adv_opts_macro">
       <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="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -85,7 +84,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathFeatureXMLToTSV_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathFeatureXMLToTSV_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -95,7 +95,7 @@
         <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
       </conditional>
       <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="short_format" value="true"/>
       <param name="best_scoring_peptide" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -104,6 +104,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathFeatureXMLToTSV_test_2 -->
     <test expect_num_outputs="2">
@@ -115,7 +118,7 @@
         <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
       </conditional>
       <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="short_format" value="false"/>
       <param name="best_scoring_peptide" value=""/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
@@ -124,6 +127,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
     <!-- TOPP_OpenSwathFeatureXMLToTSV_test_3 -->
     <test expect_num_outputs="2">
@@ -135,7 +141,7 @@
         <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
       </conditional>
       <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
-      <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta_frac="0.7" 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"/>
@@ -144,11 +150,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Converts a featureXML to a mProphet tsv.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
   <expand macro="references"/>
 </tool>