--- a/MetaProSIP.xml	Thu Dec 01 18:58:27 2022 +0000
+++ b/MetaProSIP.xml	Fri Jun 14 21:38:48 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: [Utilities]-->
+<!--Proposed Tool Section: [Quantitation]-->
 <tool id="MetaProSIP" name="MetaProSIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
+  <description>Performs proteinSIP on peptide features for elemental flux analysis</description>
   <macros>
     <token name="@EXECUTABLE@">MetaProSIP</token>
     <import>macros.xml</import>
@@ -15,13 +14,13 @@
 
 ## Preprocessing
 mkdir in_mzML &&
-ln -s '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' &&
+cp '$in_mzML' 'in_mzML/${re.sub("[^\w\-_]", "_", $in_mzML.element_identifier)}.$gxy2omsext($in_mzML.ext)' &&
 mkdir in_fasta &&
-ln -s '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
+cp '$in_fasta' 'in_fasta/${re.sub("[^\w\-_]", "_", $in_fasta.element_identifier)}.$gxy2omsext($in_fasta.ext)' &&
 mkdir out_csv &&
 mkdir out_peptide_centric_csv &&
 mkdir in_featureXML &&
-ln -s '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' &&
+cp '$in_featureXML' 'in_featureXML/${re.sub("[^\w\-_]", "_", $in_featureXML.element_identifier)}.$gxy2omsext($in_featureXML.ext)' &&
 
 ## Main program call
 
@@ -51,17 +50,17 @@
     <configfile name="hardcoded_json"><![CDATA[{"r_executable": "R", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in_mzML" type="data" format="mzml" optional="false" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
-    <param argument="-in_fasta" type="data" format="fasta" optional="false" label="Protein sequence database" help=" select fasta data sets(s)"/>
-    <param argument="-in_featureXML" type="data" format="featurexml" optional="false" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
-    <param argument="-mz_tolerance_ppm" type="float" optional="true" value="10.0" label="Tolerance in ppm" help=""/>
-    <param argument="-rt_tolerance_s" type="float" optional="true" value="30.0" label="Rolerance window around feature rt for XIC extraction" help=""/>
-    <param argument="-intensity_threshold" type="float" optional="true" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
-    <param argument="-correlation_threshold" type="float" optional="true" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
-    <param argument="-xic_threshold" type="float" optional="true" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
-    <param argument="-decomposition_threshold" type="float" optional="true" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
-    <param argument="-weight_merge_window" type="float" optional="true" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
-    <param argument="-plot_extension" type="select" optional="true" label="Extension used for plots (png|svg|pdf)" help="">
+    <param argument="-in_mzML" type="data" format="mzml" label="Centroided MS1 data" help=" select mzml data sets(s)"/>
+    <param argument="-in_fasta" type="data" format="fasta" label="Protein sequence database" help=" select fasta data sets(s)"/>
+    <param argument="-in_featureXML" type="data" format="featurexml" label="Feature data annotated with identifications (IDMapper)" help=" select featurexml data sets(s)"/>
+    <param argument="-mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help=""/>
+    <param argument="-rt_tolerance_s" type="float" value="30.0" label="Tolerance window around feature rt for XIC extraction" help=""/>
+    <param argument="-intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help=""/>
+    <param argument="-correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help=""/>
+    <param argument="-xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
+    <param argument="-decomposition_threshold" type="float" value="0.7" label="Minimum R-squared of decomposition that must be achieved for a peptide to be reported" help=""/>
+    <param argument="-weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help=""/>
+    <param argument="-plot_extension" type="select" label="Extension used for plots (png|svg|pdf)" help="">
       <option value="png" selected="true">png</option>
       <option value="svg">svg</option>
       <option value="pdf">pdf</option>
@@ -70,7 +69,7 @@
     <param argument="-qc_output_directory" type="text" optional="true" value="" label="Output directory for the quality report" help="">
       <expand macro="list_string_san" name="qc_output_directory"/>
     </param>
-    <param argument="-labeling_element" type="select" optional="true" label="Which element (single letter code) is labeled" help="">
+    <param argument="-labeling_element" type="select" label="Which element (single letter code) is labeled" help="">
       <option value="C" selected="true">C</option>
       <option value="N">N</option>
       <option value="H">H</option>
@@ -83,23 +82,23 @@
     <param argument="-filter_monoisotopic" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help=""/>
     <param argument="-cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform grouping" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-min_correlation_distance_to_averagine" type="float" optional="true" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
-      <param argument="-pattern_15N_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-pattern_13C_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-pattern_2H_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-pattern_18O_TIC_threshold" type="float" optional="true" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
-      <param argument="-heatmap_bins" type="integer" optional="true" value="20" label="Number of RIA bins for heat map generation" help=""/>
-      <param argument="-observed_peak_fraction" type="float" optional="true" value="0.5" label="Fraction of observed/expected peaks" help=""/>
-      <param argument="-min_consecutive_isotopes" type="integer" optional="true" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
-      <param argument="-score_plot_yaxis_min" type="float" optional="true" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
-      <param argument="-collect_method" type="select" optional="true" label="How RIAs are collected" help="">
+      <param argument="-min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
+      <param argument="-pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-pattern_18O_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help=""/>
+      <param argument="-heatmap_bins" type="integer" value="20" label="Number of RIA bins for heat map generation" help=""/>
+      <param argument="-observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help=""/>
+      <param argument="-min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help=""/>
+      <param argument="-score_plot_yaxis_min" type="float" value="0.0" label="The minimum value of the score axis" help="Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
+      <param argument="-collect_method" type="select" label="How RIAs are collected" help="">
         <option value="correlation_maximum" selected="true">correlation_maximum</option>
         <option value="decomposition_maximum">decomposition_maximum</option>
         <expand macro="list_string_san" name="collect_method"/>
       </param>
-      <param argument="-lowRIA_correlation_threshold" type="float" optional="true" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
+      <param argument="-lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="Disable and take correlation_threshold value for negative values"/>
       <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>
@@ -114,7 +113,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MetaProSIP_1 -->
+  <tests>
+    <!-- TOPP_MetaProSIP_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="min_correlation_distance_to_averagine" value="-1.0"/>
@@ -133,8 +133,8 @@
       </section>
       <param name="in_mzML" value="MetaProSIP_1_input.mzML"/>
       <param name="in_fasta" value="MetaProSIP_1_input.fasta"/>
-      <output name="out_csv" file="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out_csv" value="MetaProSIP_1_output_1.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="out_peptide_centric_csv" value="MetaProSIP_1_output_2.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="in_featureXML" value="MetaProSIP_1_input.featureXML"/>
       <param name="mz_tolerance_ppm" value="10.0"/>
       <param name="rt_tolerance_s" value="30.0"/>
@@ -157,11 +157,14 @@
           <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[Performs proteinSIP on peptide features for elemental flux analysis.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MetaProSIP.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MetaProSIP.html]]></help>
   <expand macro="references"/>
 </tool>