--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRewriteToFeatureXML.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,49 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.0.0">
+  <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
+
+#if $param_csv:
+  -csv $param_csv
+#end if
+#if $param_featureXML:
+  -featureXML $param_featureXML
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_FDR_cutoff:
+  -FDR_cutoff $param_FDR_cutoff
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</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 (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" 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</help>
+  <expand macro="references"/>
+</tool>