--- a/SpectraFilterWindowMower.xml	Thu Dec 01 19:00:57 2022 +0000
+++ b/SpectraFilterWindowMower.xml	Fri Jun 14 21:33:35 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: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterWindowMower" name="SpectraFilterWindowMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterWindowMower</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## 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 &&
 
 ## Main program call
@@ -39,11 +38,11 @@
     <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" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="windowsize" argument="-algorithm:windowsize" type="float" optional="true" value="50.0" label="The size of the sliding window along the m/z axis" help=""/>
-      <param name="peakcount" argument="-algorithm:peakcount" type="integer" optional="true" value="2" label="The number of peaks that should be kept" help=""/>
-      <param name="movetype" argument="-algorithm:movetype" type="select" optional="true" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="">
+      <param name="windowsize" argument="-algorithm:windowsize" type="float" value="50.0" label="The size of the sliding window along the m/z axis" help=""/>
+      <param name="peakcount" argument="-algorithm:peakcount" type="integer" value="2" label="The number of peaks that should be kept" help=""/>
+      <param name="movetype" argument="-algorithm:movetype" type="select" label="Whether sliding window (one peak steps) or jumping window (window size steps) should be used" help="">
         <option value="slide" selected="true">slide</option>
         <option value="jump">jump</option>
         <expand macro="list_string_san" name="movetype"/>
@@ -51,7 +50,7 @@
     </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>
@@ -65,14 +64,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SpectraFilterWindowMower_1 -->
+  <tests>
+    <!-- TOPP_SpectraFilterWindowMower_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="SpectraFilterWindowMower_1_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="SpectraFilterWindowMower_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="windowsize" value="50.0"/>
         <param name="peakcount" value="2"/>
@@ -84,6 +84,9 @@
           <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_SpectraFilterWindowMower_2 -->
     <test expect_num_outputs="2">
@@ -92,7 +95,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="SpectraFilterWindowMower_2_input.mzML"/>
-      <output name="out" file="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="SpectraFilterWindowMower_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="windowsize" value="20.0"/>
         <param name="peakcount" value="4"/>
@@ -104,11 +107,14 @@
           <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[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterWindowMower.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterWindowMower.html]]></help>
   <expand macro="references"/>
 </tool>