--- a/SpectraFilterParentPeakMower.xml	Thu Dec 01 19:06:48 2022 +0000
+++ b/SpectraFilterParentPeakMower.xml	Fri Jun 14 21:30:08 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: [Identification]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Applies thresholdfilter to peak spectra.</description>
+  <description>Applies thresholdfilter to peak spectra</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</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
@@ -39,20 +38,20 @@
     <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" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
-      <param name="window_size" argument="-algorithm:window_size" type="float" optional="true" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
-      <param name="default_charge" argument="-algorithm:default_charge" type="integer" optional="true" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
-      <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" optional="true" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
-      <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" optional="true" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
-      <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" optional="true" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
-      <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" optional="true" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
-      <param name="factor" argument="-algorithm:factor" type="float" optional="true" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
-      <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" optional="true" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
+      <param name="window_size" argument="-algorithm:window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
+      <param name="default_charge" argument="-algorithm:default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
+      <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
+      <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
+      <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
+      <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
+      <param name="factor" argument="-algorithm:factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
+      <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
     </section>
     <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>
@@ -66,15 +65,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
-    <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
+      <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Applies thresholdfilter to peak spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
   <expand macro="references"/>
 </tool>