--- a/DTAExtractor.xml	Thu Dec 01 19:17:40 2022 +0000
+++ b/DTAExtractor.xml	Fri Jun 14 21:43:05 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: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extracts spectra of an MS run file to several files in DTA format.</description>
+  <description>Extracts spectra of an MS run file to several files in DTA format</description>
   <macros>
     <token name="@EXECUTABLE@">DTAExtractor</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)' &&
 
 ## Main program call
 
@@ -36,22 +35,22 @@
     <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="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-out" type="text" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
       <expand macro="list_string_san" name="out"/>
     </param>
-    <param argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
+    <param argument="-mz" type="text" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
       <expand macro="list_string_san" name="mz"/>
     </param>
-    <param argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
+    <param argument="-rt" type="text" value=":" label="retention time range of spectra to extract" help="">
       <expand macro="list_string_san" name="rt"/>
     </param>
-    <param argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
+    <param argument="-level" type="text" value="1,2,3" label="MS levels to extract" help="">
       <expand macro="list_string_san" name="level"/>
     </param>
     <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>
@@ -67,7 +66,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_DTAExtractor_1 -->
+  <tests>
+    <!-- TOPP_DTAExtractor_1 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -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_DTAExtractor_2 -->
     <test expect_num_outputs="1">
@@ -102,6 +105,9 @@
           <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_DTAExtractor_3 -->
     <test expect_num_outputs="1">
@@ -120,11 +126,14 @@
           <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[Extracts spectra of an MS run file to several files in DTA format.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DTAExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DTAExtractor.html]]></help>
   <expand macro="references"/>
 </tool>