--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peak_file_converter.xml	Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,48 @@
+<tool id="openms_peak_file_convert" version="0.1.0" name="Peak List File Converter">
+  <description>
+    Converts between different MS file formats.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'FileConverter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+in_type=${in.ext}
+out=${out}
+out_type=${out_format}
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="mzml,mgf,mzxml,ms2" name="in" type="data" label="Input mzML File"/>
+    <param type="select" name="out_format" label="Output Type">
+      <option value="mzml">mzML</option>
+      <option value="mzxml">mzXML</option>
+      <option value="mgf">MGF</option>
+      <option value="ms2">MS2</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="out">
+      <change_format>
+        <when input="out_format" value="mzxml" format="mzxml" />
+        <when input="out_format" value="mgf" format="mgf" />
+        <when input="out_format" value="ms2" format="ms2" />
+      </change_format>
+    </data>
+  </outputs>
+  <help>
+**What it does**
+
+Extracts portions of the data from an mzML.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+  </help>
+</tool>