--- a/IDMerger.xml	Tue Mar 20 15:18:14 2018 -0400
+++ b/IDMerger.xml	Fri May 17 04:59:48 2019 -0400
@@ -10,12 +10,19 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>IDMerger
+  <command detect_errors="aggressive"><![CDATA[IDMerger
 
 -in
-  #for token in $param_in:
-    $token
-  #end for
+#if $merge.select_merge == 'single':
+    #for $token in $merge.param_in:
+      $token
+    #end for
+#else:
+    #for $token in $merge.inputs:
+      $token.param_in
+    #end for
+#end if
+
 #if $param_out:
   -out $param_out
 #end if
@@ -30,19 +37,27 @@
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
-  -force
+      -force
+    #end if
 #end if
-#end if
-</command>
+]]></command>
   <inputs>
-    <param name="param_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input files separated by blanks" help="(-in) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
+
+    <conditional name="merge">
+        <param help="" label="Reduce collections" name="select_merge" type="select">
+            <option selected="True" value="single">Reduce collections into one file</option>
+            <option value="repeat">Reduce collections, by aggregating single files of multiple collections</option>
+        </param>
+        <when value="single">
+            <param name="param_in" type="data" multiple="True" format="idxml" label="Input files separated by blanks" help="(-in) "/>
+        </when>
+        <when value="repeat">
+           <repeat name="inputs" min="2" title="Input idxml files">
+               <param name="param_in" type="data" format="idxml" label="Input file" help="(-in) "/>
+           </repeat>
+        </when>
+    </conditional>
+    
     <param name="param_add_to" type="data" format="idxml" optional="True" label="Optional input file" 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)"/>
     <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" 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" display="radio" type="boolean" truevalue="-pepxml_protxml" falsevalue="" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
@@ -56,5 +71,5 @@
   <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</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDMerger.html</help>
 </tool>