--- a/MascotAdapter.xml	Thu Dec 01 19:12:19 2022 +0000
+++ b/MascotAdapter.xml	Fri Jun 14 21:43:35 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: [Identification]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Annotates MS/MS spectra using Mascot.</description>
+  <description>Annotates MS/MS spectra using Mascot</description>
   <macros>
     <token name="@EXECUTABLE@">MascotAdapter</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
@@ -39,18 +38,19 @@
     <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mascotxml,mzdata" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="output file type (for TOPPAS)" help="">
+    <param argument="-in" type="data" format="mascotxml,mzdata" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select mascotxml,mzdata data sets(s)"/>
+    <param argument="-out_type" type="select" label="output file type (for TOPPAS)" help="">
       <option value="idXML">idxml</option>
       <option value="mgf">mgf</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
-    <param argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
+    <param argument="-instrument" type="text" value="Default" label="the instrument that was used to measure the spectra" help="">
       <expand macro="list_string_san" name="instrument"/>
     </param>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
-    <param argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>
-    <param argument="-taxonomy" type="select" optional="true" label="the taxonomy" help="">
+    <param argument="-precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help=""/>
+    <param argument="-peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help=""/>
+    <param argument="-taxonomy" type="select" label="the taxonomy" help="">
       <option value="All entries" selected="true">All entries</option>
       <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
       <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
@@ -126,17 +126,17 @@
       <expand macro="list_string_val" name="variable_modifications"/>
       <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-charges" type="text" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="charges"/>
       <expand macro="list_string_san" name="charges"/>
     </param>
-    <param argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help="">
+    <param argument="-db" type="text" value="MSDB" label="the database to search in" help="">
       <expand macro="list_string_san" name="db"/>
     </param>
-    <param argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help="">
+    <param argument="-hits" type="text" value="AUTO" label="the number of hits to report" help="">
       <expand macro="list_string_san" name="hits"/>
     </param>
-    <param argument="-cleavage" type="select" optional="true" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
+    <param argument="-cleavage" type="select" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
       <option value="Trypsin" selected="true">Trypsin</option>
       <option value="Arg-C">Arg-C</option>
       <option value="Asp-N">Asp-N</option>
@@ -158,27 +158,27 @@
       <option value="None">None</option>
       <expand macro="list_string_san" name="cleavage"/>
     </param>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/>
-    <param argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/>
-    <param argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/>
-    <param argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/>
-    <param argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/>
-    <param argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/>
-    <param argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/>
-    <param argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/>
-    <param argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/>
-    <param argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
+    <param argument="-missed_cleavages" type="integer" min="0" value="0" label="number of allowed missed cleavages" help=""/>
+    <param argument="-sig_threshold" type="float" value="0.05" label="significance threshold" help=""/>
+    <param argument="-pep_homol" type="float" value="1.0" label="peptide homology threshold" help=""/>
+    <param argument="-pep_ident" type="float" value="1.0" label="peptide ident threshold" help=""/>
+    <param argument="-pep_rank" type="integer" value="1" label="peptide rank" help=""/>
+    <param argument="-prot_score" type="float" value="1.0" label="protein score" help=""/>
+    <param argument="-pep_score" type="float" value="1.0" label="peptide score" help=""/>
+    <param argument="-pep_exp_z" type="integer" value="1" label="peptide expected charge" help=""/>
+    <param argument="-show_unassigned" type="integer" value="1" label="show_unassigned" help=""/>
+    <param argument="-first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
     <param argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
       <expand macro="list_string_san" name="boundary"/>
     </param>
-    <param argument="-mass_type" type="select" optional="true" label="mass type" help="">
+    <param argument="-mass_type" type="select" label="mass type" help="">
       <option value="Monoisotopic" selected="true">Monoisotopic</option>
       <option value="Average">Average</option>
       <expand macro="list_string_san" name="mass_type"/>
     </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>
@@ -196,14 +196,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MascotAdapter_1 -->
+  <tests>
+    <!-- TOPP_MascotAdapter_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="MascotAdapter_1_input.mzData"/>
-      <output name="out" file="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
+      <output name="out" value="MascotAdapter_1_output.mascot_in" compare="sim_size" delta_frac="0.7"/>
       <param name="out_type" value="mgf"/>
       <param name="instrument" value="ESI-TRAP"/>
       <param name="precursor_mass_tolerance" value="1.3"/>
@@ -233,6 +234,9 @@
           <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_MascotAdapter_2 -->
     <test expect_num_outputs="2">
@@ -241,14 +245,12 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MascotAdapter_2_input.mascotXML"/>
-      <output name="out" file="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="MascotAdapter_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="instrument" value="Default"/>
       <param name="precursor_mass_tolerance" value="2.0"/>
       <param name="peak_mass_tolerance" value="1.0"/>
       <param name="taxonomy" value="All entries"/>
-      <param name="modifications" value=""/>
-      <param name="variable_modifications" value=""/>
       <param name="charges" value="&quot;1+&quot; &quot;2+&quot; &quot;3+&quot;"/>
       <param name="db" value="MSDB"/>
       <param name="hits" value="AUTO"/>
@@ -271,11 +273,14 @@
           <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[Annotates MS/MS spectra using Mascot.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MascotAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MascotAdapter.html]]></help>
   <expand macro="references"/>
 </tool>