diff MSMS_Extractor.xml @ 0:093015b1b904 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MSMS_Extractor.xml	Mon Feb 13 02:44:05 2017 -0500
@@ -0,0 +1,26 @@
+
+<tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0">
+  <description>Removes identified scans from the mzML file using PSM report.</description>
+  <requirements>
+      <requirement type="package" version="3.0.9016">proteowizard</requirement>
+      <requirement type="package" version="3.4">pyteomics</requirement>
+  </requirements>
+  <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]}]]></command>
+  <inputs>
+    <param name="spectrumfile" type="data" format="mzml">
+      <label>Input mzML File</label>
+    </param>
+    <param name="psmreportfile" type="data" format="tabular">
+      <label>Input PSM Report File</label>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
+  </outputs>
+  
+
+  <help>
+Testing to run MSMS_Extractor script in Galaxy
+  </help>
+</tool>