diff OpenSwathRewriteToFeatureXML.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRewriteToFeatureXML.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+<?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>