--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathFeatureXMLToTSV.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,37 @@
+<?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>