--- a/PhosphoScoring.xml	Thu Dec 01 19:08:12 2022 +0000
+++ b/PhosphoScoring.xml	Fri Jun 14 21:36:07 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: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
+  <description>Scores potential phosphorylation sites in order to localize the most probable sites</description>
   <macros>
     <token name="@EXECUTABLE@">PhosphoScoring</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## 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($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,20 +42,20 @@
     <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 file with MS/MS spectra" help=" select mzml data sets(s)"/>
-    <param argument="-id" type="data" format="idxml" optional="false" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
-    <param argument="-fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
+    <param argument="-in" type="data" format="mzml" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
+    <param argument="-id" type="data" format="idxml" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
+    <param argument="-fragment_mass_tolerance" type="float" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
+    <param argument="-fragment_mass_unit" type="select" label="Unit of fragment mass tolerance" help="">
       <option value="Da" selected="true">Da</option>
       <option value="ppm">ppm</option>
       <expand macro="list_string_san" name="fragment_mass_unit"/>
     </param>
     <expand macro="adv_opts_macro">
-      <param argument="-max_peptide_length" type="integer" optional="true" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/>
-      <param argument="-max_num_perm" type="integer" optional="true" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/>
-      <param argument="-unambiguous_score" type="integer" optional="true" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/>
+      <param argument="-max_peptide_length" type="integer" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/>
+      <param argument="-max_num_perm" type="integer" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/>
+      <param argument="-unambiguous_score" type="integer" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/>
       <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>
@@ -70,16 +69,18 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="spectra.mzML"/>
-    <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
-    <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- same input as used in the MSGF+Adapter -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="spectra.mzML"/>
+      <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
+      <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
+    </test>
+  </tests>
   <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PhosphoScoring.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PhosphoScoring.html]]></help>
   <expand macro="references"/>
 </tool>