--- a/SequenceCoverageCalculator.xml	Thu Dec 01 19:22:41 2022 +0000
+++ b/SequenceCoverageCalculator.xml	Fri Jun 14 21:39:10 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: [Identification Processing]-->
 <tool id="SequenceCoverageCalculator" name="SequenceCoverageCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Prints information about idXML files.</description>
+  <description>Prints information about idXML files</description>
   <macros>
     <token name="@EXECUTABLE@">SequenceCoverageCalculator</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir in_database &&
-ln -s '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' &&
+cp '$in_database' 'in_database/${re.sub("[^\w\-_]", "_", $in_database.element_identifier)}.$gxy2omsext($in_database.ext)' &&
 mkdir in_peptides &&
-ln -s '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' &&
+cp '$in_peptides' 'in_peptides/${re.sub("[^\w\-_]", "_", $in_peptides.element_identifier)}.$gxy2omsext($in_peptides.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,11 +42,11 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_database" type="data" format="fasta" optional="false" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/>
-    <param argument="-in_peptides" type="data" format="idxml" optional="false" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
+    <param argument="-in_database" type="data" format="fasta" label="input file containing the database in FASTA format" help=" select fasta data sets(s)"/>
+    <param argument="-in_peptides" type="data" format="idxml" label="input file containing the identified peptides" help=" select idxml data sets(s)"/>
     <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>
@@ -61,16 +60,18 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- took test data from another tool that also takes idXML and fasta as input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
-    <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
-    <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- took test data from another tool that also takes idXML and fasta as input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in_database" value="PeptideIndexer_1.fasta" ftype="fasta"/>
+      <param name="in_peptides" value="SequenceCoverageCalculator_1.idXML" ftype="idxml"/>
+      <output name="out" value="SequenceCoverageCalculator.txt" ftype="txt" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Prints information about idXML files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SequenceCoverageCalculator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SequenceCoverageCalculator.html]]></help>
   <expand macro="references"/>
 </tool>