--- a/TICCalculator.xml	Thu Dec 01 19:10:31 2022 +0000
+++ b/TICCalculator.xml	Fri Jun 14 21:43:12 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="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
+  <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking)</description>
   <macros>
     <token name="@EXECUTABLE@">TICCalculator</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
 
@@ -36,8 +35,8 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
-    <param argument="-read_method" type="select" optional="true" label="Method to read the file" help="">
+    <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
+    <param argument="-read_method" type="select" label="Method to read the file" help="">
       <option value="regular" selected="true">regular</option>
       <option value="indexed">indexed</option>
       <option value="indexed_parallel">indexed_parallel</option>
@@ -49,7 +48,7 @@
     <param argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" 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>
@@ -65,7 +64,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_TICCalculator_1 -->
+  <tests>
+    <!-- TOPP_TICCalculator_1 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -80,8 +80,11 @@
           <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_TICCalculator_2 -->
+    <!-- TOPP_TICCalculator_2 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -96,8 +99,11 @@
           <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_TICCalculator_3 -->
+    <!-- TOPP_TICCalculator_3 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -112,8 +118,11 @@
           <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_TICCalculator_4 -->
+    <!-- TOPP_TICCalculator_4 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -128,8 +137,11 @@
           <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_TICCalculator_5 -->
+    <!-- TOPP_TICCalculator_5 -->
     <test expect_num_outputs="1">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -144,11 +156,14 @@
           <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[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TICCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TICCalculator.html]]></help>
   <expand macro="references"/>
 </tool>