--- a/PeakPickerIterative.xml	Thu Dec 01 18:59:31 2022 +0000
+++ b/PeakPickerIterative.xml	Fri Jun 14 21:32:08 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: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: Centroiding]-->
 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
+  <description>Finds mass spectrometric peaks in profile mass spectra</description>
   <macros>
     <token name="@EXECUTABLE@">PeakPickerIterative</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
@@ -39,21 +38,21 @@
     <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 parameters section" help="" expanded="false">
-      <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" optional="true" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
-      <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
-      <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
-      <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" optional="true" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
-      <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" optional="true" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
-      <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" optional="true" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
+      <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
+      <param name="peak_width" argument="-algorithm:peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
+      <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
+      <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
+      <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
+      <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
       <param name="check_width_internally" argument="-algorithm:check_width_internally" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help=""/>
       <param name="ms1_only" argument="-algorithm:ms1_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only do MS1" help=""/>
       <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" 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>
@@ -67,14 +66,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_PeakPickerIterative_1 -->
+  <tests>
+    <!-- TOPP_PeakPickerIterative_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="PeakPickerIterative_1_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise_" value="1.0"/>
         <param name="peak_width" value="0.04"/>
@@ -92,15 +92,18 @@
           <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>
-    <!-- UTILS_PeakPickerIterative_2 -->
+    <!-- TOPP_PeakPickerIterative_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PeakPickerIterative_2_input.mzML"/>
-      <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <param name="signal_to_noise_" value="0.0"/>
         <param name="peak_width" value="0.04"/>
@@ -118,11 +121,14 @@
           <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[Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PeakPickerIterative.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerIterative.html]]></help>
   <expand macro="references"/>
 </tool>