<?xml version='1.0' encoding='UTF-8'?>
<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="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 $param_best_scoring_peptide:
  -best_scoring_peptide     "$param_best_scoring_peptide"
#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 name="param_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_tr" type="data" format="traml" optional="False" label="TraML transition file" help="(-tr) "/>
    <param name="param_short_format" type="boolean" truevalue="-short_format" falsevalue="" checked="false" optional="True" label="Whether to write short (one peptide per line) or long format (one transition per line)" help="(-short_format) "/>
    <param name="param_best_scoring_peptide" type="text" size="30" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="tabular"/>
  </outputs>
  <help>**What it does**

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>
  <expand macro="references"/>
</tool>