--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DecoyDatabase.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,80 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="DecoyDatabase" name="DecoyDatabase" version="2.0.0">
+  <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
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_decoy_string:
+  -decoy_string     "$param_decoy_string"
+#end if
+#if $param_decoy_string_position:
+  -decoy_string_position
+  #if " " in str($param_decoy_string_position):
+    "$param_decoy_string_position"
+  #else
+    $param_decoy_string_position
+  #end if
+#end if
+#if $param_append:
+  -append
+#end if
+#if $param_shuffle:
+  -shuffle
+#end if
+-threads \${GALAXY_SLOTS:-24} 
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input FASTA file(s), each containing a database" help="(-in) It is recommended to include a contaminant database as well">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_decoy_string" type="text" size="30" value="_rev" label="String that is appended to the accession of the protein database to indicate a decoy protein" help="(-decoy_string) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <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" falsevalue="" 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" falsevalue="" checked="false" optional="True" label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" help="(-shuffle) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" 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</help>
+  <expand macro="references"/>
+</tool>