diff IDMassAccuracy.xml @ 16:0819fd9da302 draft default tip

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

--- a/IDMassAccuracy.xml	Thu Dec 01 18:58:59 2022 +0000
+++ b/IDMassAccuracy.xml	Fri Jun 14 21:31:46 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: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
+  <description>Calculates a distribution of the mass error from given mass spectra and IDs</description>
   <macros>
     <token name="@EXECUTABLE@">IDMassAccuracy</token>
     <import>macros.xml</import>
@@ -17,16 +16,16 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir id_in_cond.id_in &&
 #if $id_in_cond.id_in_select == "no"
 mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} && 
-${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
+${' '.join(["cp '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
 #else
-ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
+cp '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
 #end if
 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_precursor &&
@@ -106,10 +105,10 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" multiple="true" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
+        <param argument="-in" type="data" format="mzml" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
       </when>
     </conditional>
     <conditional name="id_in_cond">
@@ -118,19 +117,19 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
+        <param argument="-id_in" type="data" format="idxml" multiple="true" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-id_in" type="data" format="idxml" multiple="false" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
+        <param argument="-id_in" type="data" format="idxml" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
       </when>
     </conditional>
     <param argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
     <param argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
+    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
     <expand macro="adv_opts_macro">
-      <param argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
+      <param argument="-number_of_bins" type="integer" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" 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>
@@ -162,7 +161,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDMassAccuracy_1 -->
+  <tests>
+    <!-- TOPP_IDMassAccuracy_1 -->
     <test expect_num_outputs="5">
       <section name="adv_opts">
         <param name="number_of_bins" value="10"/>
@@ -175,24 +175,27 @@
       <conditional name="id_in_cond">
         <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
       </conditional>
-      <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_precursor" value="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="precursor_error_ppm" value="false"/>
-      <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_fragment" value="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="fragment_error_ppm" value="false"/>
       <param name="fragment_mass_tolerance" value="0.5"/>
-      <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
-      <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_precursor_fit" value="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_fragment_fit" value="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <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[Calculates a distribution of the mass error from given mass spectra and IDs.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDMassAccuracy.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMassAccuracy.html]]></help>
   <expand macro="references"/>
 </tool>