--- a/hicPlotMatrix.xml	Mon Apr 03 07:06:13 2017 -0400
+++ b/hicPlotMatrix.xml	Thu Nov 02 11:09:46 2017 -0400
@@ -5,8 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command>
-<![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         ln -s '$matrix' input_matrix.h5 &&
 
         @BINARY@
@@ -22,17 +21,17 @@
             #end if
 
 
-            --outFileName plot.svg
+            --outFileName plot.$image_file_format
 
             $perChromosome
             $clearMaskedBins
 
-            --whatToShow $whatToShow.whatToShow_select
+            --whatToShow '$whatToShow.whatToShow_select'
 
 
             ## special: --chromosomeOrder is optional, but if given needs at least one argument
             #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
-            #if chroms
+            #if chroms:
                 --chromosomeOrder '$chroms'
             #end if
 
@@ -63,7 +62,7 @@
                     --zMax $whatToShow.zMax
                 #end if
             #end if
-
+        && mv plot.$image_file_format plot
 ]]>
     </command>
     <inputs>
@@ -91,9 +90,11 @@
             <when value="heatmap"/>
         </conditional>
 
-        <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):"
-            help="This option overrides --region and --region2">
-            <param name="chromosome" type="text" />
+        <repeat name="chromosomeOrder" min="0" title="Chromosomes to include (and order to plot in):"
+            help="This option overrides --region and --region2" >
+            <param name="chromosome" type="text" >
+                <validator type="empty_field" />
+            </param>
         </repeat>
 
         <param argument="--region" type="text" optional="True" label="Plot only this region"
@@ -107,10 +108,17 @@
 
         <param argument="--vMin" type="float" optional="true" label="vMin"/>
         <param argument="--vMax" type="float" optional="true" label="vMax"/>
-
+        <param name="image_file_format" type="select" label="Image output format">
+            <option value="png" selected="True">png</option>
+            <option value="svg">svg</option>
+        </param>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="plot.svg" format="svg" label="${tool.name} on ${on_string}"/>
+        <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="image_file_format" value="svg" format="svg" />
+            </change_format>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -120,14 +128,15 @@
             <param name="log1p" value="True"/>
             <param name="clearMaskedBins" value="True"/>
             <param name="whatToShow_select" value="heatmap"/>
-            <output name="outFileName" file="hicPlotMatrix_result1.svg" ftype="svg" compare="sim_size"/>
+            <param name="image_file_format" value="png" />
+            <output name="outFileName" file="master_matrix_plot.png" ftype="png" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
 
 **What it does**
 
-Plots a HiC matrix heatmap.
+Plots a Hi-C matrix heatmap.
 
 ]]></help>
     <expand macro="citations" />