<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="OpenSwathRewriteToFeatureXML" docurl="http://www.openms.de/documentation/UTILS_OpenSwathRewriteToFeatureXML.html" category="Targeted Experiments" >
<description><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.]]></description>
<manual><![CDATA[Combines featureXML and mProphet tsv to FDR filtered featureXML.]]></manual>
<citations>
  <citation doi="10.1038/nmeth.3959" url="" />
</citations>
<PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="OpenSwathRewriteToFeatureXML" description="Combines featureXML and mProphet tsv to FDR filtered featureXML.">
    <ITEM name="version" value="2.6.0-pre-exported-20201001" 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;OpenSwathRewriteToFeatureXML&apos;">
      <ITEM name="csv" value="" type="input-file" description="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" required="false" advanced="false" supported_formats="*.csv" />
      <ITEM name="featureXML" value="" type="input-file" description="input featureXML file" required="true" advanced="false" supported_formats="*.featureXML" />
      <ITEM name="out" value="" type="output-file" description="output featureXML file" required="true" advanced="false" supported_formats="*.featureXML" />
      <ITEM name="FDR_cutoff" value="-1.0" type="double" description="FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" 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="bool" description="Disables progress logging to command line" required="false" advanced="true" />
      <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" />
      <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" />
    </NODE>
  </NODE>
</PARAMETERS>
</tool>