--- a/IDMerger.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/IDMerger.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,37 +1,57 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="IDMerger" name="IDMerger" version="1.12.0">
-  <description>Merges several protein/peptide identification files into one file.</description>
-  <macros>
-    <token name="@EXECUTABLE@">IDMerger</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>IDMerger
+<?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: [File Handling]-->
+  <tool id="IDMerger" name="IDMerger" version="2.0.0">
+    <description>Merges several protein/peptide identification files into one file.</description>
+    <macros>
+      <token name="@EXECUTABLE@">IDMerger</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>IDMerger
 
--in ${param_in}
--out ${param_out}
--add_to ${param_add_to}
-${param_annotate_file_origin}
-${param_pepxml_protxml}
--threads \${GALAXY_SLOTS:-24} 
+-in
+$param_in1
+#for $infile in $inputs
+    $infile.param_in
+#end for
+  -out $param_out
+#if $param_add_to:
+  -add_to $param_add_to
+#end if
+#if $param_annotate_file_origin:
+  -annotate_file_origin
+#end if
+#if $param_pepxml_protxml:
+  -pepxml_protxml
+#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="idXML" optional="False" size="20" label="Input files separated by blanks" help="(-in)"/>
-    <param name="param_add_to" type="data" format="idXML" optional="True" label="Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)." help="(-add_to)"/>
-    <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin true" falsevalue="-annotate_file_origin false" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)." help="(-annotate_file_origin)"/>
-    <param name="param_pepxml_protxml" type="boolean" truevalue="-pepxml_protxml true" falsevalue="-pepxml_protxml false" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file.#br#Exactly two input files are expected in this case. Not compatible with 'add_to'." help="(-pepxml_protxml)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Output file" format="idXML"/>
-  </outputs>
-  <help>**What it does**
+    <inputs>
+<param name="param_in1" type="data" format="idxml" label="Input files" help="(-in)" /> 
+    <repeat name="inputs" title="Input files">
+	<param name="param_in" type="data" format="idxml" label="Input files" help="(-in)" />
+    </repeat>
 
-Merges several protein/peptide identification files into one file.
+      <param format="xml" help="(-add_to) IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)" label="Optional input file" name="param_add_to" optional="True" type="data"/>
+      <param checked="false" falsevalue="" help="(-annotate_file_origin) " label="Store the original filename in each protein/peptide identification (meta value: file_origin)" name="param_annotate_file_origin" optional="True" truevalue="-annotate_file_origin" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'" label="Merge idXML files derived from a pepXML and corresponding protXML file" name="param_pepxml_protxml" optional="True" truevalue="-pepxml_protxml" 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="xml" name="param_out"/>
+    </outputs>
+    <help>Merges several protein/peptide identification files into one file.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html</help>
+  </tool>