--- a/BaselineFilter.xml	Thu Dec 01 19:10:21 2022 +0000
+++ b/BaselineFilter.xml	Fri Jun 14 21:37:37 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: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Removes the baseline from profile spectra using a top-hat filter.</description>
+  <description>Removes the baseline from profile spectra using a top-hat filter</description>
   <macros>
     <token name="@EXECUTABLE@">BaselineFilter</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 &&
 
 ## Main program call
@@ -39,14 +38,14 @@
     <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 raw data file" help=" select mzml data sets(s)"/>
-    <param argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
-    <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help="">
+    <param argument="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
+    <param argument="-struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
+    <param argument="-struc_elem_unit" type="select" label="Unit of 'struc_elem_length' paramete" help="">
       <option value="Thomson" selected="true">Thomson</option>
       <option value="DataPoints">DataPoints</option>
       <expand macro="list_string_san" name="struc_elem_unit"/>
     </param>
-    <param argument="-method" type="select" optional="true" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
+    <param argument="-method" type="select" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
       <option value="identity">identity</option>
       <option value="erosion">erosion</option>
       <option value="dilation">dilation</option>
@@ -61,7 +60,7 @@
     </param>
     <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>
@@ -75,14 +74,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_BaselineFilter_1 -->
+  <tests>
+    <!-- TOPP_BaselineFilter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="BaselineFilter_input.mzML"/>
-      <output name="out" file="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="struc_elem_length" value="1.5"/>
       <param name="struc_elem_unit" value="Thomson"/>
       <param name="method" value="tophat"/>
@@ -92,11 +92,14 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_BaselineFilter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_BaselineFilter.html]]></help>
   <expand macro="references"/>
 </tool>