--- a/MRMMapper.xml	Thu Dec 01 19:06:17 2022 +0000
+++ b/MRMMapper.xml	Fri Jun 14 21:45:15 2024 +0000
@@ -1,6 +1,5 @@
-<?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="MRMMapper" name="MRMMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
   <macros>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir tr &&
-ln -s '$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
@@ -43,17 +42,17 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
-    <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file containing chromatograms (converted mzXML file)" help=" select mzml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" optional="true" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
-      <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" optional="true" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
+      <param name="precursor_tolerance" argument="-algorithm:precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help=""/>
+      <param name="product_tolerance" argument="-algorithm:product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help=""/>
       <param name="map_multiple_assays" argument="-algorithm:map_multiple_assays" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow to map multiple assays to chromatograms and duplicate these chromatograms in the output" help=""/>
       <param name="error_on_unmapped" argument="-algorithm:error_on_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat remaining, unmapped chromatograms as an erro" help=""/>
     </section>
     <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>
@@ -67,7 +66,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MRMMapper_test_1 -->
+  <tests>
+    <!-- TOPP_MRMMapper_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -75,7 +75,7 @@
       </section>
       <param name="in" value="MRMMapping_input.chrom.mzML"/>
       <param name="tr" value="MRMMapping_input.TraML"/>
-      <output name="out" file="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MRMMapping_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="precursor_tolerance" value="0.3"/>
         <param name="product_tolerance" value="0.3"/>
@@ -88,6 +88,9 @@
           <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_MRMMapper_test_2 -->
     <test expect_num_outputs="2">
@@ -97,7 +100,7 @@
       </section>
       <param name="in" value="MRMMapping_input.chrom.mzML"/>
       <param name="tr" value="MRMMapping_input_2.TraML"/>
-      <output name="out" file="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MRMMapping_output_2.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="precursor_tolerance" value="0.01"/>
         <param name="product_tolerance" value="0.01"/>
@@ -110,11 +113,14 @@
           <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[MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MRMMapper.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MRMMapper.html]]></help>
   <expand macro="references"/>
 </tool>