<?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 CTD2Galaxy.-->
  <!--Proposed Tool Section: [Targeted Experiments]-->
  <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="2.0.0">
    <description>Converts a featureXML to a mProphet tsv.</description>
    <macros>
      <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>OpenSwathFeatureXMLToTSV

-in
  #for token in $param_in:
    $token
  #end for
#if $param_tr:
  -tr $param_tr
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_short_format:
  -short_format
#end if
#if $param_best_scoring_peptide:
  -best_scoring_peptide     &quot;$param_best_scoring_peptide&quot;
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param format="traml" help="(-tr) " label="TraML transition file" name="param_tr" optional="False" type="data"/>
      <param checked="false" falsevalue="" help="(-short_format) " label="Whether to write short (one peptide per line) or long format (one transition per line)" name="param_short_format" optional="True" truevalue="-short_format" type="boolean"/>
      <param help="(-best_scoring_peptide) " label="If only the best scoring feature per peptide should be printed, give the variable name" name="param_best_scoring_peptide" size="30" type="text">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="tabular" name="param_out"/>
    </outputs>
    <help>Converts a featureXML to a mProphet tsv.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html</help>
  </tool>