--- a/IDSplitter.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IDSplitter.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,38 +1,45 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="IDSplitter" name="IDSplitter" version="1.12.0">
-  <description>Splits protein/peptide identifications off of annotated data files</description>
-  <macros>
-    <token name="@EXECUTABLE@">IDSplitter</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>IDSplitter
+<?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="IDSplitter" name="IDSplitter" version="2.0.0">
+    <description>Splits protein/peptide identifications off of annotated data files</description>
+    <macros>
+      <token name="@EXECUTABLE@">IDSplitter</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>IDSplitter
 
--in ${param_in}
--out ${param_out}
--id_out ${param_id_out}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_id_out:
+  -id_out $param_id_out
+#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="mzML,featureXML,consensusXML" optional="False" label="Input file (data annotated with identifications)" help="(-in)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file (data without identifications). Either 'out' or 'id_out' are required. They can be used together." format="consensusXML">
-      <change_format>
-        <when input="param_out_type" value="mzML" format="mzML"/>
-        <when input="param_out_type" value="featureXML" format="featureXML"/>
-      </change_format>
-    </data>
-    <data name="param_id_out" label="Output file (identifications). Either 'out' or 'id_out' are required. They can be used together." format="idXML"/>
-  </outputs>
-  <help>**What it does**
-
-Splits protein/peptide identifications off of annotated data files
+    <inputs>
+      <param format="xml,consensusxml,mzml" help="(-in) " label="Input file (data annotated with identifications)" name="param_in" optional="False" type="data"/>
+      <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="input" metadata_source="param_in" name="param_out"/>
+      <data format="xml" name="param_id_out"/>
+    </outputs>
+    <help>Splits protein/peptide identifications off of annotated data files
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDSplitter.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDSplitter.html</help>
+  </tool>