--- a/MapAlignerPoseClustering.xml	Thu Jan 11 18:08:16 2018 -0500
+++ b/MapAlignerPoseClustering.xml	Mon Feb 12 10:28:56 2018 -0500
@@ -7,10 +7,24 @@
   <expand macro="stdio"/>
   <expand macro="requirements"/>
   <command><![CDATA[
+
+  mkdir -p ./results_trafoxml ./results_out &&
   MapAlignerPoseClustering
--in $param_in
--out $out
--trafo_out $trafo_out
+
+-in
+#for $infile in $param_in:
+    '$infile'
+#end for
+
+-out
+#for $counter,$infile in enumerate($param_in):
+    ./results_out/${infile.element_identifier}.${infile.extension}
+#end for
+
+-trafo_out
+#for $counter,$infile in enumerate($param_in):
+    ./results_trafoxml/${infile.element_identifier}.trafoxml
+#end for
 
 -threads "\${GALAXY_SLOTS:-1}"
 
@@ -97,10 +111,11 @@
   #end if
 #end if
 #end if
+
  ]]>
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mzML,featureXML" label="Input files to align (all must have the same file type)" help="(-in) "/>
+    <param name="param_in" type="data" format="mzML,featureXML" multiple="true" label="Input files to align (all must have the same file type)" help="(-in) "/>
     <param name="param_reference_file" type="data" format="mzML,featureXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file) "/>
     <param name="param_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
     <param name="param_algorithm_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map" help="(-max_num_peaks_considered) To use all, set to '-1'"/>
@@ -134,8 +149,13 @@
     </expand>
     </inputs>
     <outputs>
-        <data name="out" format_source="param_in" metadata_source="param_in" />
-        <data name="trafo_out" format_source="param_in" metadata_source="param_in" />
+        <collection name="out" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="results_out"/>
+        </collection>
+
+        <collection name="trafo_out" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="results_trafoxml"/>
+        </collection>
     </outputs>
     <help>Corrects retention time distortions between maps using a pose clustering approach.