--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/decoy_database.xml	Fri May 10 17:31:05 2013 -0400
@@ -0,0 +1,53 @@
+<tool id="openms_decoy_database" version="0.1.0" name="Decoy Database Creator">
+  <description>
+    Create decoy protein/peptide databases from normal ones.
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <expand macro="requires" />
+  <command interpreter="python">
+    openms_wrapper.py --executable 'DecoyDatabase' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+out=${out}
+decoy_string=${decoy_string}
+decoy_string_position=${decoy_string_position}
+append=${append}
+shuffle=${shuffle}
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="fasta" name="in" type="data" label="Input database"/>
+    <param name="decoy_string" type="text" value="_rev" label="Decoy string"/>
+    <param name="decoy_string_position" type="select" label="Decoy Position">
+      <option value="suffix" selected="true">Suffix</option>
+      <option value="prefix">Prefix</option>
+    </param>
+    <param type="boolean" name="append" label="Append to original database" checked="true" />
+    <param type="select" name="shuffle" label="Decoy type">
+      <option value="false" selected="true">Reverse</option>
+      <option value="true">Shuffle</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="out" />
+  </outputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal" description="Error creating decoy database." />
+  </stdio>  
+  <help>
+**What it does**
+
+Create decoy protein/peptide databases from normal ones.
+
+**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>