--- a/computeMatrix.xml	Mon Aug 05 11:36:11 2013 -0400
+++ b/computeMatrix.xml	Tue Aug 06 08:20:47 2013 -0400
@@ -4,14 +4,29 @@
     <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <command>
+    #import tempfile
+
+    #set $temp_input_handle = tempfile.NamedTemporaryFile()
+    #set $temp_input_path = $temp_input_handle.name
+    #silent $temp_input_handle.close()
+
+    #for $rf in $regionsFiles:
+        cat "$rf.regionsFile" >> $temp_input_path;
+        #if str($rf.label.value).strip():
+            echo "\#$rf.label.value" >> $temp_input_path;
+        #else:
+            echo "\#$rf.regionsFile.name" >> $temp_input_path;
+        #end if
+    #end for
+
+
   computeMatrix
 
   $mode.mode_select
-  --regionsFileName '$regionsFile'
+  --regionsFileName '$temp_input_path'
   --scoreFileName '$scoreFile'
   --outFileName '$outFileName'
 
-  ##ToDo
   --numberOfProcessors 4
 
   #if $output.showOutputSettings == "yes"
@@ -61,11 +76,17 @@
     #end if
 
   #end if
+  ; rm $temp_input_path
 
   </command>
   <inputs>
-    <param name="regionsFile" format="bed,gff" type="data" label="Regions to plot" help="File, in BED or GFF format, containing the regions to plot."/>
-    <param name="scoreFile" format="bigwig,bam" type="data" label="Score file" help="Either a bigWig file (containing a score, usually covering the whole genome) or a BAM file. For this last case, coverage counts will be used for the heatmap."/>
+
+    <repeat name="regionsFiles" title="regions to plot" min="1">
+        <param name="regionsFile" format="bed" type="data" label="Regions to plot" help="File, in BED or GFF format, containing the regions to plot."/>
+        <param name="label" type="text" size="30" optional="true" value="" label="Label" help="Label to use in the output."/>
+    </repeat>
+
+    <param name="scoreFile" format="bigwig" type="data" label="Score file" help="Either a bigWig file (containing a score, usually covering the whole genome) or a BAM file. For this last case, coverage counts will be used for the heatmap."/>
 
     <conditional name="mode" >
       <param name="mode_select" type="select" label="computeMatrix has two main output options" help="In the scale-regions mode, all regions in the BED/GFF file are stretched or shrunk to the same length (bp) that is indicated by the user. Reference-point refers to a position within the BED/GFF regions (e.g start of region). In the reference-point mode only those genomic positions before (downstream) and/or after (upstream) the reference point will be plotted.">