diff PrecursorMassCorrector.xml @ 13:b71e9103d269 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

--- a/PrecursorMassCorrector.xml	Thu Dec 01 18:58:17 2022 +0000
+++ b/PrecursorMassCorrector.xml	Fri Jun 14 21:28:46 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: [Mass Correction and Calibration]-->
 <tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
+  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information</description>
   <macros>
     <token name="@EXECUTABLE@">PrecursorMassCorrector</token>
     <import>macros.xml</import>
@@ -15,11 +14,11 @@
 
 ## 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 $feature_in:
   mkdir feature_in &&
-  ln -s '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' &&
+  cp '$feature_in' 'feature_in/${re.sub("[^\w\-_]", "_", $feature_in.element_identifier)}.$gxy2omsext($feature_in.ext)' &&
 #end if
 
 ## Main program call
@@ -47,14 +46,14 @@
     <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 mzML file containing the spectra" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="Input mzML file containing the spectra" help=" select mzml data sets(s)"/>
     <param argument="-feature_in" type="data" format="featurexml" optional="true" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries" help="will be matched to the feature m/z values if possible select featurexml data sets(s)"/>
-    <param argument="-precursor_mass_tolerance" type="float" optional="true" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/>
+    <param argument="-precursor_mass_tolerance" type="float" min="0.0" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;" help="this value should be set to the instruments selection window"/>
     <expand macro="adv_opts_macro">
-      <param argument="-max_charge" type="integer" optional="true" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/>
-      <param argument="-intensity_threshold" type="float" optional="true" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/>
+      <param argument="-max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help=""/>
+      <param argument="-intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help=""/>
       <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>
@@ -68,7 +67,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_PrecursorMassCorrector_1 -->
+  <tests>
+    <!-- TOPP_PrecursorMassCorrector_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="max_charge" value="3"/>
@@ -77,7 +77,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="PrecursorMassCorrector_1_input.mzML"/>
-      <output name="out" file="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="PrecursorMassCorrector_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="precursor_mass_tolerance" value="1.5"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -85,11 +85,14 @@
           <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[Corrects the precursor entries of MS/MS spectra, by using MS1 information.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PrecursorMassCorrector.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PrecursorMassCorrector.html]]></help>
   <expand macro="references"/>
 </tool>