--- a/SeedListGenerator.xml	Thu Dec 01 19:04:23 2022 +0000
+++ b/SeedListGenerator.xml	Fri Jun 14 21:39:33 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: [Quantitation]-->
 <tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Generates seed lists for feature detection.</description>
+  <description>Generates seed lists for feature detection</description>
   <macros>
     <token name="@EXECUTABLE@">SeedListGenerator</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_prefix &&
 
 ## Main program call
@@ -38,11 +37,11 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file (see below for details)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
     <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
     <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>
@@ -58,10 +57,11 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SeedListGenerator_1 -->
+  <tests>
+    <!-- TOPP_SeedListGenerator_1 -->
     <!-- TOPP_SeedListGenerator_2 -->
     <!-- TOPP_SeedListGenerator_3 -->
-  <test expect_num_outputs="2">
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -76,7 +76,8 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -91,7 +92,8 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -108,10 +110,10 @@
         </assert_contents>
       </output>
     </test>
-</tests>
+  </tests>
   <help><![CDATA[Generates seed lists for feature detection.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SeedListGenerator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SeedListGenerator.html]]></help>
   <expand macro="references"/>
 </tool>