<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.1.0" name="OpenSwathFeatureXMLToTSV" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathFeatureXMLToTSV.html" category="Targeted Experiments" >
<description><![CDATA[Converts a featureXML to a mProphet tsv.]]></description>
<manual><![CDATA[Converts a featureXML to a mProphet tsv.]]></manual>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="OpenSwathFeatureXMLToTSV" description="Converts a featureXML to a mProphet tsv.">
    <ITEM name="version" value="2.1.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;OpenSwathFeatureXMLToTSV&apos;">
      <ITEMLIST name="in" type="input-file" description="Input files separated by blank" required="true" advanced="false" supported_formats="*.featureXML">
      </ITEMLIST>
      <ITEM name="tr" value="" type="input-file" description="TraML transition file" required="true" advanced="false" supported_formats="*.traML" />
      <ITEM name="out" value="" type="output-file" description="tsv output file (mProphet compatible)" required="true" advanced="false" supported_formats="*.csv" />
      <ITEM name="short_format" value="false" type="string" description="Whether to write short (one peptide per line) or long format (one transition per line)." required="false" advanced="false" restrictions="true,false" />
      <ITEM name="best_scoring_peptide" value="" type="string" description="If only the best scoring feature per peptide should be printed, give the variable name" required="false" advanced="false" />
      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
