--- a/id_merger.xml	Wed Dec 19 00:33:53 2012 -0500
+++ b/id_merger.xml	Fri May 10 17:31:05 2013 -0400
@@ -2,27 +2,23 @@
   <description>
     Merges several idXML files into one idXML file.
   </description>
-  <requirements>
-    <requirement type="package">openms</requirement>
-  </requirements>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <expand macro="requires" />
   <command interpreter="python">
     openms_wrapper.py --executable 'IDMerger' --config $config
   </command>
   <configfiles>
     <configfile name="config">[simple_options]
-#set $in_str = ""      
-#for $input in $inputs
-#set $in_str = $input.input + " " $in_str
-#end for
-in="${in_str}"
+in=${",".join(map(str, $inputs))}
 out=${out}
 annotate_file_origin=${annotate_file_origin}
 </configfile>
   </configfiles>
   <inputs>
-    <repeat name="inputs">
-      <param format="idxml" name="input" type="data" label="idXML Input"/>
-    </repeat>
+    <param format="idxml" name="inputs" type="data" label="idXML Inputs" multiple="true" />
     <param type="boolean" name="annotate_file_origin" label="Annotate file origin" help="Store the original filename in each protein/peptide identification (MetaValue: file_origin)." />
   </inputs>
   <outputs>