--- a/QCCalculator.xml	Thu Dec 01 19:09:47 2022 +0000
+++ b/QCCalculator.xml	Fri Jun 14 21:34:05 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: [Utilities]-->
+<!--Proposed Tool Section: []-->
 <tool id="QCCalculator" name="QCCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
+  <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection</description>
   <macros>
     <token name="@EXECUTABLE@">QCCalculator</token>
     <import>macros.xml</import>
@@ -15,19 +14,19 @@
 
 ## 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 $id:
   mkdir id &&
-  ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+  cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 #end if
 #if $feature:
   mkdir feature &&
-  ln -s '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
+  cp '$feature' 'feature/${re.sub("[^\w\-_]", "_", $feature.element_identifier)}.$gxy2omsext($feature.ext)' &&
 #end if
 #if $consensus:
   mkdir consensus &&
-  ln -s '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
+  cp '$consensus' 'consensus/${re.sub("[^\w\-_]", "_", $consensus.element_identifier)}.$gxy2omsext($consensus.ext)' &&
 #end if
 
 ## Main program call
@@ -63,13 +62,14 @@
     <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="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
+    <param argument="-in" type="data" format="mzml" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help=" select mzml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension or content" help="">
       <option value="mzQC">mzqc</option>
       <option value="qcML">qcml</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-label" type="text" optional="true" value="label" label="unique name for the run that can be used in a figure label" help="">
+    <param argument="-label" type="text" value="label" label="unique name for the run that can be used in a figure label" help="">
       <expand macro="list_string_san" name="label"/>
     </param>
     <param argument="-name" type="text" optional="true" value="" label="name of the person creating this mzQC file" help="">
@@ -87,7 +87,7 @@
     <param argument="-remove_duplicate_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="This flag should be set, if you work with a set of merged features" help=""/>
     <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>
@@ -105,14 +105,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_QCCalculator_1 -->
+  <tests>
+    <!-- TOPP_QCCalculator_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="QCCalculator_input.mzML"/>
-      <output name="out" file="QCCalculator_1.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/>
+      <output name="out" value="QCCalculator_1_output.qcML" compare="sim_size" delta_frac="0.7" ftype="qcml"/>
       <param name="out_type" value="qcML"/>
       <param name="label" value="label"/>
       <param name="name" value=""/>
@@ -125,15 +126,18 @@
           <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>
-    <!-- UTILS_QCCalculator_2 -->
+    <!-- TOPP_QCCalculator_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="QCCalculator_input.mzML"/>
-      <output name="out" file="QCCalculator_2.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/>
+      <output name="out" value="QCCalculator_2_output.mzQC" compare="sim_size" delta_frac="0.7" ftype="mzqc"/>
       <param name="out_type" value="mzQC"/>
       <param name="label" value="label"/>
       <param name="name" value="name"/>
@@ -148,33 +152,39 @@
           <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>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <param name="out_type" value="qcML"/>
-    <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,consensusXML input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
-    <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
-    <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
-    <param name="out_type" value="qcML"/>
-    <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
-  </test>
-  <test expect_num_outputs="1"><!-- took test data from another test w mzML,idXML,featureXML input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
-    <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
-    <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
-    <param name="out_type" value="qcML"/>
-    <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
-  </test>
-</tests>
+    <test expect_num_outputs="1">
+      <!-- took test data from another test w mzML input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
+      <param name="out_type" value="qcML"/>
+      <output name="out" ftype="qcml" value="QCCalculator1.qcML" compare="sim_size" delta="250"/>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- took test data from another test w mzML,idXML,consensusXML input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="OpenPepXL_input.mzML"/>
+      <param name="id" ftype="idxml" value="OpenPepXL_output.idXML"/>
+      <param name="consensus" ftype="consensusxml" value="OpenPepXL_input.consensusXML"/>
+      <param name="out_type" value="qcML"/>
+      <output name="out" ftype="qcml" value="QCCalculator2.qcML" compare="sim_size" delta="250"/>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- took test data from another test w mzML,idXML,featureXML input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="IDMapper_4_input.mzML"/>
+      <param name="id" ftype="idxml" value="IDMapper_4_input.idXML"/>
+      <param name="feature" ftype="featurexml" value="IDMapper_4_input.featureXML"/>
+      <param name="out_type" value="qcML"/>
+      <output name="out" ftype="qcml" value="QCCalculator3.qcML" compare="sim_size" delta="250"/>
+    </test>
+  </tests>
   <help><![CDATA[Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCCalculator.html]]></help>
   <expand macro="references"/>
 </tool>