--- a/NoiseFilterSGolay.xml	Thu Dec 01 19:05:55 2022 +0000
+++ b/NoiseFilterSGolay.xml	Fri Jun 14 21:37:07 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="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description>
+  <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data</description>
   <macros>
     <token name="@EXECUTABLE@">NoiseFilterSGolay</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
@@ -39,19 +38,19 @@
     <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="-in" type="data" format="mzml" label="input raw data file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="frame_length" argument="-algorithm:frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
-      <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/>
+      <param name="frame_length" argument="-algorithm:frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
+      <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param argument="-processOption" type="select" optional="true" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
+      <param argument="-processOption" type="select" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
         <option value="inmemory" selected="true">inmemory</option>
         <option value="lowmemory">lowmemory</option>
         <expand macro="list_string_san" name="processOption"/>
       </param>
       <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>
@@ -65,7 +64,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_NoiseFilterSGolay_1 -->
+  <tests>
+    <!-- TOPP_NoiseFilterSGolay_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="processOption" value="inmemory"/>
@@ -73,7 +73,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="9"/>
         <param name="polynomial_order" value="4"/>
@@ -84,6 +84,9 @@
           <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>
     <!-- TOPP_NoiseFilterSGolay_2 -->
     <test expect_num_outputs="2">
@@ -93,7 +96,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="11"/>
         <param name="polynomial_order" value="4"/>
@@ -104,6 +107,9 @@
           <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>
     <!-- TOPP_NoiseFilterSGolay_3 -->
     <test expect_num_outputs="2">
@@ -113,7 +119,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_1_input.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="9"/>
         <param name="polynomial_order" value="4"/>
@@ -124,6 +130,9 @@
           <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>
     <!-- TOPP_NoiseFilterSGolay_4 -->
     <test expect_num_outputs="2">
@@ -133,7 +142,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="NoiseFilterSGolay_2_input.chrom.mzML"/>
-      <output name="out" file="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="NoiseFilterSGolay_2_output.chrom.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="frame_length" value="11"/>
         <param name="polynomial_order" value="4"/>
@@ -144,11 +153,14 @@
           <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 noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_NoiseFilterSGolay.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NoiseFilterSGolay.html]]></help>
   <expand macro="references"/>
 </tool>