--- a/hicPlotViewpoint.xml	Fri Apr 27 08:43:05 2018 -0400
+++ b/hicPlotViewpoint.xml	Sat Jun 09 15:34:08 2018 -0400
@@ -7,18 +7,29 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        hicPlotViewpoint --matrix '$matrix_h5_cooler'
+        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+            ln -s '$m' ${counter}_matrix &&
+        #end for
+        #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+
+        hicPlotViewpoint --matrix "$m"
         #if $interactionOutFileName:
-            $interactionOutFileName interactions.bedgraph
+            $interactionOutFileName interactions
         #end if
         --outFileName plot.$image_file_format
         --region $region
         --referencePoint $referencePoint
         && mv plot.$image_file_format plot
+        && ls -lah
+        #if $interactionOutFileName:
+            #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+                && mv interactions_${counter}_matrix.bedgraph ${counter}_interactions.bedgraph
+            #end for
+        #end if
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_macro' />
+        <expand macro='matrix_h5_cooler_multiple_macro' />
         <expand macro="region" />
         <param name="referencePoint" type="text" label="Reference point"
             help="The format is chr:referencePoint or chr:regionStart-regionEnd."/>
@@ -33,34 +44,37 @@
     </inputs>
     <outputs>
 
-        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Plot">
+        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} [${on_string}]: Plot">
             <change_format>
                 <when input="image_file_format" value="png" format="png" />
                 <when input="image_file_format" value="svg" format="svg" />
             </change_format>
         </data>
-        <data name='interactionFile' from_work_dir='interactions.bedgraph' format='bedgraph' label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: Bedgraph">
+
+        <data format="bedgraph" name="interactionFile" >
+            <discover_datasets pattern='(?P&lt;designation&gt;.+)\_interactions\.bedgraph' directory="." visible="true"/>
             <filter>interactionOutFileName</filter>
         </data>
 
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000' />
             <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
-            <param name="matrix_h5_cooler" value="Li_et_al_2015.h5"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000-3300000' />
             <param name='interactionOutFileName' value='True' />
             <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
-            <output name="interactionFile" file="li_32-33mb_interactions.bedgraph" ftype="bedgraph" compare="sim_size"/>
-
+            <output name="interactionFile">
+                <discovered_dataset designation="0" file="li_32-33mb_interactions.bedgraph" />
+            </output>
         </test>
     </tests>
     <help><![CDATA[