--- a/RNPxlXICFilter.xml	Thu Dec 01 19:24:09 2022 +0000
+++ b/RNPxlXICFilter.xml	Fri Jun 14 21:30:53 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: [Cross-Linking]-->
 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
+  <description>Remove MS2 spectra from treatment based on the fold change between control and treatment</description>
   <macros>
     <token name="@EXECUTABLE@">RNPxlXICFilter</token>
     <import>macros.xml</import>
@@ -15,9 +14,9 @@
 
 ## Preprocessing
 mkdir control &&
-ln -s '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' &&
+cp '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' &&
 mkdir treatment &&
-ln -s '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' &&
+cp '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,14 +42,14 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
-    <param argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/>
-    <param argument="-rt_tol" type="float" optional="true" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
-    <param argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
+    <param argument="-control" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-treatment" type="data" format="mzml" label="input mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-fold_change" type="float" value="2.0" label="fold change between XICs" help=""/>
+    <param argument="-rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
+    <param argument="-mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" 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>
@@ -64,16 +63,18 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
+    </test>
+  </tests>
   <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNPxlXICFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNPxlXICFilter.html]]></help>
   <expand macro="references"/>
 </tool>