view OpenSwathFeatureXMLToTSV.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="1.12.0">
  <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 ${param_in}
-tr ${param_tr}
-out ${param_out}
${param_short_format}
-best_scoring_peptide ${param_best_scoring_peptide}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML" optional="False" size="20" label="Input files separated by blank" help="(-in)"/>
    <param name="param_tr" type="data" format="" optional="False" label="TraML transition file" help="(-tr)"/>
    <param name="param_short_format" type="boolean" truevalue="-short_format true" falsevalue="-short_format false" 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="20" label="If only the best scoring feature per peptide should be printed, give the variable name" help="(-best_scoring_peptide)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="tsv output file (mProphet compatible)" 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

@REFERENCES@
</help>
</tool>