--- a/OpenSwathChromatogramExtractor.xml	Thu Dec 01 19:13:34 2022 +0000
+++ b/OpenSwathChromatogramExtractor.xml	Fri Jun 14 21:41:20 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: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extract chromatograms (XIC) from a MS2 map file.</description>
+  <description>Extract chromatograms (XIC) from a MS2 map file</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
     <import>macros.xml</import>
@@ -17,15 +16,15 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 #if $rt_norm:
   mkdir rt_norm &&
-  ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
+  cp '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
 #end if
 mkdir out &&
 
@@ -66,23 +65,23 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input files separated by blank" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input files separated by blank" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
+    <param argument="-tr" type="data" format="csv,traml" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
     <param argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
-    <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
-    <param argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
-    <param argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
-    <param argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
+    <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
+    <param argument="-rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
+    <param argument="-ion_mobility_window" type="float" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
+    <param argument="-mz_window" type="float" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
     <param argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
     <param argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
     <param argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
     <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
-      <param name="type" argument="-model:type" type="select" optional="true" label="Type of model" help="">
+      <param name="type" argument="-model:type" type="select" label="Type of model" help="">
         <option value="linear" selected="true">linear</option>
         <option value="b_spline">b_spline</option>
         <option value="interpolated">interpolated</option>
@@ -92,13 +91,13 @@
       <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-extraction_function" type="select" optional="true" label="Function used to extract the signal" help="">
+      <param argument="-extraction_function" type="select" label="Function used to extract the signal" help="">
         <option value="tophat" selected="true">tophat</option>
         <option value="bartlett">bartlett</option>
         <expand macro="list_string_san" name="extraction_function"/>
       </param>
       <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>
@@ -112,7 +111,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_OpenSwathChromatogramExtractor_test_1 -->
+  <tests>
+    <!-- TOPP_OpenSwathChromatogramExtractor_test_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="extraction_function" value="tophat"/>
@@ -123,7 +123,7 @@
         <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -141,6 +141,9 @@
           <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_OpenSwathChromatogramExtractor_test_2 -->
     <test expect_num_outputs="2">
@@ -154,7 +157,7 @@
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
       <param name="rt_norm" value="OpenSwathChromatogramExtractor_input.trafoXML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_output_2.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="50.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -172,6 +175,9 @@
           <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_OpenSwathChromatogramExtractor_test_3 -->
     <test expect_num_outputs="2">
@@ -184,7 +190,7 @@
         <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_output_3.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -202,6 +208,9 @@
           <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_OpenSwathChromatogramExtractor_test_4 -->
     <test expect_num_outputs="2">
@@ -214,7 +223,7 @@
         <param name="in" value="OpenSwathChromatogramExtractor_4_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_4_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="0.05"/>
@@ -232,6 +241,9 @@
           <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_OpenSwathChromatogramExtractor_test_5 -->
     <test expect_num_outputs="2">
@@ -244,7 +256,7 @@
         <param name="in" value="OpenSwathChromatogramExtractor_input.mzML"/>
       </conditional>
       <param name="tr" value="OpenSwathChromatogramExtractor_5_input.TraML"/>
-      <output name="out" file="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="OpenSwathChromatogramExtractor_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="min_upper_edge_dist" value="0.0"/>
       <param name="rt_window" value="-1.0"/>
       <param name="ion_mobility_window" value="-1.0"/>
@@ -262,11 +274,14 @@
           <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[Extract chromatograms (XIC) from a MS2 map file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
   <expand macro="references"/>
 </tool>