--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pepxml_protxml_merger.xml	Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,37 @@
+<tool id="openms_pepxml_protxml_merger" version="0.1.0" name="Merge idXML from PepXML and ProtXML">
+  <description>
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'IDMerger' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in="${pepxml} ${protxml}"
+out=${out}
+annotate_file_origin=${annotate_file_origin}
+pepxml_protxml=true
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="idxml" name="pepxml" type="data" label="idXML from PepXML"/>
+    <param format="idxml" name="protxml" type="data" label="idXML from ProtXML"/>
+    <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." />
+  </inputs>
+  <outputs>
+    <data format="idxml" name="out" />
+  </outputs>
+  <help>
+**What it does**
+
+Merge idXML files derived from a pepXML and corresponding protXML file.
+
+**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>