--- a/IDMapper.xml	Thu Dec 01 19:05:34 2022 +0000
+++ b/IDMapper.xml	Fri Jun 14 21:39:26 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: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDMapper" name="IDMapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Assigns protein/peptide identifications to features or consensus features.</description>
+  <description>Assigns protein/peptide identifications to features or consensus features</description>
   <macros>
     <token name="@EXECUTABLE@">IDMapper</token>
     <import>macros.xml</import>
@@ -15,13 +14,13 @@
 
 ## Preprocessing
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 #if $spectra._in:
   mkdir spectra.in &&
-  ln -s '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' &&
+  cp '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' &&
 #end if
 
 ## Main program call
@@ -51,16 +50,16 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-id" type="data" format="idxml,mzid" optional="false" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/>
-    <param argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
-    <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
-    <param argument="-mz_tolerance" type="float" optional="true" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
-    <param argument="-mz_measure" type="select" optional="true" label="Unit of 'mz_tolerance'" help="">
+    <param argument="-id" type="data" format="idxml,mzid" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,mzq" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
+    <param argument="-rt_tolerance" type="float" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
+    <param argument="-mz_tolerance" type="float" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
+    <param argument="-mz_measure" type="select" label="Unit of 'mz_tolerance'" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="mz_measure"/>
     </param>
-    <param argument="-mz_reference" type="select" optional="true" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
+    <param argument="-mz_reference" type="select" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
       <option value="precursor">precursor</option>
       <option value="peptide" selected="true">peptide</option>
       <expand macro="list_string_san" name="mz_reference"/>
@@ -79,7 +78,7 @@
     <expand macro="adv_opts_macro">
       <param argument="-ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help=""/>
       <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>
@@ -93,7 +92,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDMapper_1 -->
+  <tests>
+    <!-- TOPP_IDMapper_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="ignore_charge" value="true"/>
@@ -102,7 +102,7 @@
       </section>
       <param name="id" value="IDMapper_1_input.idXML"/>
       <param name="in" value="IDMapper_1_input.featureXML"/>
-      <output name="out" file="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDMapper_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="rt_tolerance" value="5.0"/>
       <param name="mz_tolerance" value="1.0"/>
       <param name="mz_measure" value="Da"/>
@@ -122,6 +122,9 @@
           <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_IDMapper_2 -->
     <test expect_num_outputs="2">
@@ -132,7 +135,7 @@
       </section>
       <param name="id" value="IDMapper_2_input.idXML"/>
       <param name="in" value="IDMapper_2_input.consensusXML"/>
-      <output name="out" file="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDMapper_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="rt_tolerance" value="5.0"/>
       <param name="mz_tolerance" value="1.0"/>
       <param name="mz_measure" value="Da"/>
@@ -152,6 +155,9 @@
           <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_IDMapper_3 -->
     <test expect_num_outputs="2">
@@ -162,7 +168,7 @@
       </section>
       <param name="id" value="IDMapper_3_input.idXML"/>
       <param name="in" value="IDMapper_3_input.featureXML"/>
-      <output name="out" file="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDMapper_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="rt_tolerance" value="4.0"/>
       <param name="mz_tolerance" value="3.0"/>
       <param name="mz_measure" value="ppm"/>
@@ -182,75 +188,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test>
-    <!-- TOPP_IDMapper_4 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="id" value="IDMapper_4_input.idXML"/>
-      <param name="in" value="IDMapper_4_input.featureXML"/>
-      <output name="out" file="IDMapper_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="rt_tolerance" value="10.0"/>
-      <param name="mz_tolerance" value="20.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="true"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_4_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <is_valid_xml/>
-        </assert_contents>
-      </output>
-    </test>
-    <!-- TOPP_IDMapper_5 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="ignore_charge" value="false"/>
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="id" value="IDMapper_5_input.idXML"/>
-      <param name="in" value="IDMapper_5_input.featureXML"/>
-      <output name="out" file="IDMapper_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <param name="rt_tolerance" value="20.0"/>
-      <param name="mz_tolerance" value="10.0"/>
-      <param name="mz_measure" value="ppm"/>
-      <param name="mz_reference" value="peptide"/>
-      <section name="feature">
-        <param name="use_centroid_rt" value="false"/>
-        <param name="use_centroid_mz" value="false"/>
-      </section>
-      <section name="consensus">
-        <param name="use_subelements" value="false"/>
-        <param name="annotate_ids_with_subelements" value="false"/>
-      </section>
-      <section name="spectra">
-        <param name="_in" value="IDMapper_5_input.mzML"/>
-      </section>
-      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-      <output name="ctd_out" ftype="xml">
-        <assert_contents>
-          <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[Assigns protein/peptide identifications to features or consensus features.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMapper.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMapper.html]]></help>
   <expand macro="references"/>
 </tool>