--- a/HighResPrecursorMassCorrector.xml	Thu Dec 01 19:01:37 2022 +0000
+++ b/HighResPrecursorMassCorrector.xml	Fri Jun 14 21:40:04 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: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Mass Correction and Calibration]-->
 <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects the precursor mass and charge determined by the instrument software.</description>
+  <description>Corrects the precursor mass and charge determined by the instrument software</description>
   <macros>
     <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
     <import>macros.xml</import>
@@ -15,14 +14,14 @@
 
 ## 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($in.ext)' &&
 mkdir out &&
 #if "out_csv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_csv &&
 #end if
 #if $feature.in:
   mkdir feature.in &&
-  ln -s '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' &&
+  cp '$feature.in' 'feature.in/${re.sub("[^\w\-_]", "_", $feature.in.element_identifier)}.$gxy2omsext($feature.in.ext)' &&
 #end if
 
 ## Main program call
@@ -60,32 +59,32 @@
     <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 (centroided data)" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input file (centroided data)" help=" select mzml data sets(s)"/>
     <section name="feature" title="Use features for precursor mass correction" help="" expanded="false">
       <param name="in" argument="-feature:in" type="data" format="featurexml" optional="true" label="Features used to correct precursor masses" help=" select featurexml data sets(s)"/>
-      <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" optional="true" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
-      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance" argument="-feature:mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="Used to determine matching to feature mass traces"/>
+      <param name="mz_tolerance_unit" argument="-feature:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
       </param>
-      <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" optional="true" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
-      <param name="max_trace" argument="-feature:max_trace" type="integer" optional="true" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
+      <param name="rt_tolerance" argument="-feature:rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help=""/>
+      <param name="max_trace" argument="-feature:max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help=""/>
       <param name="believe_charge" argument="-feature:believe_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assume precursor charge to be correct" help=""/>
       <param name="keep_original" argument="-feature:keep_original" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help=""/>
       <param name="assign_all_matching" argument="-feature:assign_all_matching" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="Only evaluated if copies are created (feature:keep_original)"/>
     </section>
     <section name="nearest_peak" title="Use nearest centroided MS1 peak for precursor mass correction" help="" expanded="false">
-      <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance" argument="-nearest_peak:mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(Disable method by setting value to 0.0)"/>
+      <param name="mz_tolerance_unit" argument="-nearest_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
       </param>
     </section>
     <section name="highest_intensity_peak" title="Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction" help="" expanded="false">
-      <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" optional="true" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
-      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+      <param name="mz_tolerance" argument="-highest_intensity_peak:mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the highest intensity MS1 peak" help="Suggested value 1/max. expected charge. (Disable method by setting value to 0.0)"/>
+      <param name="mz_tolerance_unit" argument="-highest_intensity_peak:mz_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
         <option value="Da">Da</option>
         <option value="ppm" selected="true">ppm</option>
         <expand macro="list_string_san" name="mz_tolerance_unit"/>
@@ -93,7 +92,7 @@
     </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>
@@ -111,14 +110,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_HighResPrecursorMassCorrector_1 -->
+  <tests>
+    <!-- TOPP_HighResPrecursorMassCorrector_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_2860_1103_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_2860_1103_3.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -143,39 +143,9 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test>
-    <!-- TOPP_HighResPrecursorMassCorrector_2 -->
-    <test expect_num_outputs="2">
-      <section name="adv_opts">
-        <param name="force" value="false"/>
-        <param name="test" value="true"/>
-      </section>
-      <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_1035_1178_4_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
-      <section name="feature">
-        <param name="in" value="HighResPrecursorMassCorrector_1035_1178_4.featureXML"/>
-        <param name="mz_tolerance" value="10.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-        <param name="rt_tolerance" value="0.0"/>
-        <param name="max_trace" value="4"/>
-        <param name="believe_charge" value="false"/>
-        <param name="keep_original" value="false"/>
-        <param name="assign_all_matching" value="false"/>
-      </section>
-      <section name="nearest_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </section>
-      <section name="highest_intensity_peak">
-        <param name="mz_tolerance" value="0.0"/>
-        <param name="mz_tolerance_unit" value="ppm"/>
-      </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>
     <!-- TOPP_HighResPrecursorMassCorrector_3 -->
     <test expect_num_outputs="2">
@@ -184,7 +154,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_2538_1091_2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_2538_1091_2.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -209,6 +179,9 @@
           <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_HighResPrecursorMassCorrector_4 -->
     <test expect_num_outputs="2">
@@ -217,7 +190,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_2810_1091_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_2810_1091_3.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -242,6 +215,9 @@
           <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_HighResPrecursorMassCorrector_5 -->
     <test expect_num_outputs="2">
@@ -250,7 +226,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_3070_1191_3_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="in" value="HighResPrecursorMassCorrector_3070_1191_3.featureXML"/>
         <param name="mz_tolerance" value="5.0"/>
@@ -275,6 +251,9 @@
           <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_HighResPrecursorMassCorrector_6 -->
     <test expect_num_outputs="2">
@@ -283,7 +262,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="HighResPrecursorMassCorrector_6.mzML"/>
-      <output name="out" file="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="HighResPrecursorMassCorrector_6_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="feature">
         <param name="mz_tolerance" value="5.0"/>
         <param name="mz_tolerance_unit" value="ppm"/>
@@ -307,11 +286,14 @@
           <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[Corrects the precursor mass and charge determined by the instrument software.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_HighResPrecursorMassCorrector.html]]></help>
   <expand macro="references"/>
 </tool>