--- a/NovorAdapter.xml	Thu Dec 01 19:20:30 2022 +0000
+++ b/NovorAdapter.xml	Fri Jun 14 21:45:52 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 of Proteins/Peptides (SearchEngines)]-->
 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Performs de novo sequencing of peptides from MS/MS data with Novor.</description>
+  <description>Performs de novo sequencing of peptides from MS/MS data with Novor</description>
   <macros>
     <token name="@EXECUTABLE@">NovorAdapter</token>
     <import>macros.xml</import>
@@ -15,11 +14,11 @@
 
 ## 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 &&
 #if $novorFile:
   mkdir novorFile &&
-  ln -s '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
+  cp '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
 #end if
 
 ## Main program call
@@ -47,30 +46,30 @@
     <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
-    <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme - currently only Trypsin is supported" help="">
+    <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
+    <param argument="-enzyme" type="select" label="Digestion enzyme - currently only Trypsin is supported" help="">
       <option value="Trypsin" selected="true">Trypsin</option>
       <expand macro="list_string_san" name="enzyme"/>
     </param>
-    <param argument="-fragmentation" type="select" optional="true" label="Fragmentation method" help="">
+    <param argument="-fragmentation" type="select" label="Fragmentation method" help="">
       <option value="CID" selected="true">CID</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragmentation"/>
     </param>
-    <param argument="-massAnalyzer" type="select" optional="true" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
+    <param argument="-massAnalyzer" type="select" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
       <option value="Trap" selected="true">Trap</option>
       <option value="TOF">TOF</option>
       <option value="FT">FT</option>
       <expand macro="list_string_san" name="massAnalyzer"/>
     </param>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
-    <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
+    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Fragmentation error tolerance  (Da)" help=""/>
+    <param argument="-precursor_mass_tolerance" type="float" value="15.0" label="Precursor error tolerance  (ppm or Da)" help=""/>
+    <param argument="-precursor_error_units" type="select" label="Unit of precursor mass tolerance" help="">
       <option value="ppm" selected="true">ppm</option>
       <option value="Da">Da</option>
       <expand macro="list_string_san" name="precursor_error_units"/>
     </param>
-    <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help="">
+    <param argument="-variable_modifications" type="select" multiple="true" optional="true" label="Variable modifications" help="">
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Amidated (C-term)">Amidated (C-term)</option>
@@ -99,7 +98,7 @@
       <option value="Trimethyl (RK)">Trimethyl (RK)</option>
       <expand macro="list_string_san" name="variable_modifications"/>
     </param>
-    <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help="">
+    <param argument="-fixed_modifications" type="select" multiple="true" optional="true" label="Fixed modifications" help="">
       <option value="Acetyl (K)">Acetyl (K)</option>
       <option value="Acetyl (N-term)">Acetyl (N-term)</option>
       <option value="Amidated (C-term)">Amidated (C-term)</option>
@@ -128,7 +127,7 @@
       <option value="Trimethyl (RK)">Trimethyl (RK)</option>
       <expand macro="list_string_san" name="fixed_modifications"/>
     </param>
-    <param argument="-forbiddenResidues" display="checkboxes" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help="">
+    <param argument="-forbiddenResidues" type="select" multiple="true" optional="true" label="Forbidden Resiudes" help="">
       <option value="I">I</option>
       <option value="U">U</option>
       <expand macro="list_string_san" name="forbiddenResidues"/>
@@ -136,7 +135,7 @@
     <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt 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>
@@ -150,11 +149,12 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_NovorAdapter_1 -->
+  <tests>
+    <!-- TOPP_NovorAdapter_1 -->
   </tests>
   <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NovorAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NovorAdapter.html]]></help>
   <expand macro="references"/>
 </tool>