--- a/DecoyDatabase.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/DecoyDatabase.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,42 +1,80 @@
-<?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
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Utilities]-->
+  <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="references"/>
+    <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} 
+-in
+  #for token in $param_in:
+    $token
+  #end for
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_decoy_string:
+  -decoy_string     &quot;$param_decoy_string&quot;
+#end if
+#if $param_decoy_string_position:
+  -decoy_string_position
+  #if &quot; &quot; in str($param_decoy_string_position):
+    &quot;$param_decoy_string_position&quot;
+  #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" 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.
+    <inputs>
+      <param format="fasta" help="(-in) It is recommended to include a contaminant database as well" label="Input FASTA file(s), each containing a database" multiple="true" name="param_in" optional="False" size="30" type="data">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-decoy_string) " label="String that is appended to the accession of the protein database to indicate a decoy protein" name="param_decoy_string" size="30" type="text" value="_rev">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-decoy_string_position) " label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" name="param_decoy_string_position" optional="True" type="select" value="suffix">
+        <option value="prefix">prefix</option>
+        <option value="suffix">suffix</option>
+      </param>
+      <param checked="false" falsevalue="" help="(-append) " label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" name="param_append" optional="True" truevalue="-append" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-shuffle) " label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" name="param_shuffle" optional="True" truevalue="-shuffle" type="boolean"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="fasta" name="param_out"/>
+    </outputs>
+    <help>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>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
+  </tool>