--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DecoyDatabase.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,42 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="DecoyDatabase" name="DecoyDatabase" version="1.12.0">
+  <description>Create decoy peptide databases from normal ones.</description>
+  <macros>
+    <token name="@EXECUTABLE@">DecoyDatabase</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>DecoyDatabase
+
+-in ${param_in}
+-out ${param_out}
+-decoy_string ${param_decoy_string}
+-decoy_string_position ${param_decoy_string_position}
+${param_append}
+${param_shuffle}
+-threads \${GALAXY_SLOTS:-24} 
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="fasta" optional="False" size="20" label="Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well." help="(-in)"/>
+    <param name="param_decoy_string" type="text" size="20" value="_rev" label="String that is appended to the accession of the protein database to indicate a decoy protein." help="(-decoy_string)"/>
+    <param name="param_decoy_string_position" type="select" optional="True" value="suffix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position)">
+      <option value="prefix">prefix</option>
+      <option value="suffix">suffix</option>
+    </param>
+    <param name="param_append" type="boolean" truevalue="-append true" falsevalue="-append false" checked="false" optional="True" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches." help="(-append)"/>
+    <param name="param_shuffle" type="boolean" truevalue="-shuffle true" falsevalue="-shuffle false" checked="false" optional="True" label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" help="(-shuffle)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output FASTA file where the decoy database will be written to." format="fasta"/>
+  </outputs>
+  <help>**What it does**
+
+Create decoy peptide databases from normal ones.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html
+
+@REFERENCES@
+</help>
+</tool>