--- a/MassCalculator.xml	Thu Dec 01 19:08:33 2022 +0000
+++ b/MassCalculator.xml	Fri Jun 14 21:36:45 2024 +0000
@@ -1,6 +1,5 @@
-<?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: [Misc / Helpers]-->
 <tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
   <macros>
@@ -16,7 +15,7 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
@@ -57,10 +56,10 @@
       <expand macro="list_string_val" name="in_seq"/>
       <expand macro="list_string_san" name="in_seq"/>
     </param>
-    <param argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-charge" type="text" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_integer_valsan" name="charge"/>
     </param>
-    <param argument="-format" type="select" optional="true" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
+    <param argument="-format" type="select" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
       <option value="list" selected="true">list</option>
       <option value="table">table</option>
       <option value="mass_only">mass_only</option>
@@ -68,7 +67,7 @@
       <expand macro="list_string_san" name="format"/>
     </param>
     <param argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/>
-    <param argument="-fragment_type" type="select" optional="true" label="For what type of sequence/fragment the mass should be computed" help="">
+    <param argument="-fragment_type" type="select" label="For what type of sequence/fragment the mass should be computed" help="">
       <option value="full" selected="true">full</option>
       <option value="internal">internal</option>
       <option value="N-terminal">N-terminal</option>
@@ -86,7 +85,7 @@
     </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>
@@ -106,15 +105,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_MassCalculator_1 -->
+  <tests>
+    <!-- TOPP_MassCalculator_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="MassCalculator_1_input.tsv" ftype="tabular"/>
-      <param name="in_seq" value=""/>
-      <output name="out" file="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="MassCalculator_1_output.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="charge" value="0 1"/>
       <param name="format" value="table"/>
       <param name="average_mass" value="false"/>
@@ -126,15 +125,18 @@
           <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_MassCalculator_2 -->
+    <!-- TOPP_MassCalculator_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in_seq" value="&quot;LDQWLC(Carbamidomethyl)EKL&quot; &quot;(Glu-&gt;pyro-Glu)EAM(Oxidation)APKHK&quot; &quot;RANVM(Oxidation)DYR&quot; &quot;FGVEQDVDMVFASFIR&quot;"/>
-      <output name="out" file="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out" value="MassCalculator_2_output.txt" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="charge" value="1 2 3"/>
       <param name="format" value="list"/>
       <param name="average_mass" value="false"/>
@@ -146,11 +148,14 @@
           <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 masses and mass-to-charge ratios of peptide sequences
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MassCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MassCalculator.html]]></help>
   <expand macro="references"/>
 </tool>