<?xml version='1.0' encoding='UTF-8'?>
<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="1.12.0">
  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
  <macros>
    <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>OpenSwathRewriteToFeatureXML

-csv ${param_csv}
-featureXML ${param_featureXML}
-out ${param_out}
-FDR_cutoff ${param_FDR_cutoff}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv)"/>
    <param name="param_featureXML" type="data" format="featureXML" optional="False" label="input featureXML file" help="(-featureXML)"/>
    <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here)" help="(-FDR_cutoff)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output featureXML file" format="featureXML"/>
  </outputs>
  <help>**What it does**

Combines featureXML and mProphet tsv to FDR filtered featureXML.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathRewriteToFeatureXML.html

@REFERENCES@
</help>
</tool>