--- a/ExternalCalibration.xml	Thu Dec 01 19:03:40 2022 +0000
+++ b/ExternalCalibration.xml	Fri Jun 14 21:38:02 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="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies an external mass recalibration.</description>
+  <description>Applies an external mass recalibration</description>
   <macros>
     <token name="@EXECUTABLE@">ExternalCalibration</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
@@ -39,16 +38,16 @@
     <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 peak file" help=" select mzml data sets(s)"/>
-    <param argument="-offset" type="float" optional="true" value="0.0" label="Mass offset in ppm" help=""/>
-    <param argument="-slope" type="float" optional="true" value="0.0" label="Slope (dependent on m/z)" help=""/>
-    <param argument="-power" type="float" optional="true" value="0.0" label="Power (dependent on m/z)" help=""/>
-    <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-in" type="data" format="mzml" label="Input peak file" help=" select mzml data sets(s)"/>
+    <param argument="-offset" type="float" value="0.0" label="Mass offset in ppm" help=""/>
+    <param argument="-slope" type="float" value="0.0" label="Slope (dependent on m/z)" help=""/>
+    <param argument="-power" type="float" value="0.0" label="Power (dependent on m/z)" help=""/>
+    <param argument="-ms_level" type="text" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="ms_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>
@@ -62,14 +61,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_ExternalCalibration_1_MS1 -->
+  <tests>
+    <!-- TOPP_ExternalCalibration_1_MS1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="offset" value="-5.5"/>
       <param name="slope" value="0.0001"/>
       <param name="power" value="0.0"/>
@@ -80,6 +80,9 @@
           <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_ExternalCalibration_2_MS2 -->
     <test expect_num_outputs="2">
@@ -88,7 +91,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="ExternalCalibration_1_input.mzML"/>
-      <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="offset" value="-5.5"/>
       <param name="slope" value="0.0001"/>
       <param name="power" value="0.0"/>
@@ -99,11 +102,14 @@
           <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 an external mass recalibration.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ExternalCalibration.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ExternalCalibration.html]]></help>
   <expand macro="references"/>
 </tool>