--- a/FeatureFinderMetabo.xml	Thu Dec 01 19:24:19 2022 +0000
+++ b/FeatureFinderMetabo.xml	Fri Jun 14 21:42:49 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: [Quantitation]-->
 <tool id="FeatureFinderMetabo" name="FeatureFinderMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.</description>
+  <description>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMetabo</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($in.ext)' &&
 mkdir out &&
 #if "out_chrom_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_chrom &&
@@ -52,52 +51,52 @@
     <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="Centroided mzML file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Centroided mzML file" help=" select mzml data sets(s)"/>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
       <section name="common" title="Common parameters for all other subsections" help="" expanded="false">
-        <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" optional="true" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
-        <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" optional="true" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
-        <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" optional="true" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
+        <param name="noise_threshold_int" argument="-algorithm:common:noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help=""/>
+        <param name="chrom_peak_snr" argument="-algorithm:common:chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help=""/>
+        <param name="chrom_fwhm" argument="-algorithm:common:chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help=""/>
       </section>
       <section name="mtd" title="Mass Trace Detection parameters" help="" expanded="false">
-        <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" optional="true" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
+        <param name="mass_error_ppm" argument="-algorithm:mtd:mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help=""/>
         <param name="reestimate_mt_sd" argument="-algorithm:mtd:reestimate_mt_sd" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help=""/>
-        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" optional="true" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
+        <param name="quant_method" argument="-algorithm:mtd:quant_method" type="select" label="Method of quantification for mass traces" help="For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace">
           <option value="area" selected="true">area</option>
           <option value="median">median</option>
           <option value="max_height">max_height</option>
           <expand macro="list_string_san" name="quant_method"/>
         </param>
-        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" optional="true" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
+        <param name="trace_termination_criterion" argument="-algorithm:mtd:trace_termination_criterion" type="select" label="Termination criterion for the extension of mass traces" help="In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
           <option value="outlier" selected="true">outlier</option>
           <option value="sample_rate">sample_rate</option>
           <expand macro="list_string_san" name="trace_termination_criterion"/>
         </param>
-        <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" optional="true" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
-        <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" optional="true" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
-        <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" optional="true" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
-        <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" optional="true" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
+        <param name="trace_termination_outliers" argument="-algorithm:mtd:trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help=""/>
+        <param name="min_sample_rate" argument="-algorithm:mtd:min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help=""/>
+        <param name="min_trace_length" argument="-algorithm:mtd:min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help=""/>
+        <param name="max_trace_length" argument="-algorithm:mtd:max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="Set to a negative value to disable maximal length check during mass trace detection"/>
       </section>
       <section name="epd" title="Elution Profile Detection (to separate isobaric Mass Traces by elution time)" help="" expanded="false">
         <param name="enabled" argument="-algorithm:epd:enabled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable splitting of isobaric mass traces by chromatographic peak detection" help="Disable for direct injection"/>
-        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" optional="true" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
+        <param name="width_filtering" argument="-algorithm:epd:width_filtering" type="select" label="Enable filtering of unlikely peak widths" help="The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
           <option value="off">off</option>
           <option value="fixed" selected="true">fixed</option>
           <option value="auto">auto</option>
           <expand macro="list_string_san" name="width_filtering"/>
         </param>
-        <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" optional="true" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
-        <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" optional="true" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
+        <param name="min_fwhm" argument="-algorithm:epd:min_fwhm" type="float" value="1.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
+        <param name="max_fwhm" argument="-algorithm:epd:max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="Ignored if parameter width_filtering is off or auto"/>
         <param name="masstrace_snr_filtering" argument="-algorithm:epd:masstrace_snr_filtering" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply post-filtering by signal-to-noise ratio after smoothing" help=""/>
       </section>
       <section name="ffm" title="FeatureFinder parameters (assembling mass traces to charged features)" help="" expanded="false">
-        <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" optional="true" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
-        <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" optional="true" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/>
-        <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" optional="true" value="1" label="Lowest charge state to conside" help=""/>
-        <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" optional="true" value="3" label="Highest charge state to conside" help=""/>
+        <param name="local_rt_range" argument="-algorithm:ffm:local_rt_range" type="float" value="10.0" label="RT range where to look for coeluting mass traces" help=""/>
+        <param name="local_mz_range" argument="-algorithm:ffm:local_mz_range" type="float" value="6.5" label="MZ range where to look for isotopic mass traces" help=""/>
+        <param name="charge_lower_bound" argument="-algorithm:ffm:charge_lower_bound" type="integer" value="1" label="Lowest charge state to conside" help=""/>
+        <param name="charge_upper_bound" argument="-algorithm:ffm:charge_upper_bound" type="integer" value="3" label="Highest charge state to conside" help=""/>
         <param name="report_summed_ints" argument="-algorithm:ffm:report_summed_ints" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone" help=""/>
         <param name="enable_RT_filtering" argument="-algorithm:ffm:enable_RT_filtering" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require sufficient overlap in RT while assembling mass traces" help="Disable for direct injection data"/>
-        <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" optional="true" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
+        <param name="isotope_filtering_model" argument="-algorithm:ffm:isotope_filtering_model" type="select" label="Remove/score candidate assemblies based on isotope intensities" help="SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device">
           <option value="metabolites (2% RMS)">metabolites (2% RMS)</option>
           <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
           <option value="peptides">peptides</option>
@@ -109,14 +108,14 @@
         <param name="report_convex_hulls" argument="-algorithm:ffm:report_convex_hulls" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help=""/>
         <param name="remove_single_traces" argument="-algorithm:ffm:remove_single_traces" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassembled traces (single traces)" help=""/>
         <param name="mz_scoring_by_elements" argument="-algorithm:ffm:mz_scoring_by_elements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the m/z range of the assumed elements to detect isotope peaks" help="A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'"/>
-        <param name="elements" argument="-algorithm:ffm:elements" type="text" optional="true" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help="">
+        <param name="elements" argument="-algorithm:ffm:elements" type="text" value="CHNOPS" label="Elements assumes to be present in the sample (this influences isotope detection)" help="">
           <expand macro="list_string_san" name="elements"/>
         </param>
       </section>
     </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>
@@ -134,14 +133,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FeatureFinderMetabo_1 -->
+  <tests>
+    <!-- TOPP_FeatureFinderMetabo_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="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetabo_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -187,6 +187,9 @@
           <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_FeatureFinderMetabo_2 -->
     <test expect_num_outputs="2">
@@ -195,7 +198,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_2_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetabo_2_noEPD_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="100.0"/>
@@ -241,6 +244,9 @@
           <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_FeatureFinderMetabo_3 -->
     <test expect_num_outputs="3">
@@ -249,8 +255,8 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FeatureFinderMetabo_3.tmp" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="FeatureFinderMetabo_3_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -296,6 +302,9 @@
           <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_FeatureFinderMetabo_4 -->
     <test expect_num_outputs="3">
@@ -304,8 +313,8 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_3_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="out_chrom" file="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FeatureFinderMetabo_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out_chrom" value="FeatureFinderMetabo_4_chrom_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -351,6 +360,9 @@
           <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_FeatureFinderMetabo_5 -->
     <test expect_num_outputs="2">
@@ -359,7 +371,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="FeatureFinderMetabo_1_input.mzML"/>
-      <output name="out" file="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FeatureFinderMetabo_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <section name="algorithm">
         <section name="common">
           <param name="noise_threshold_int" value="10.0"/>
@@ -405,11 +417,14 @@
           <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[Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMetabo.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureFinderMetabo.html]]></help>
   <expand macro="references"/>
 </tool>