--- a/computeMatrix.xml	Tue Dec 10 12:13:18 2013 -0500
+++ b/computeMatrix.xml	Sat Dec 14 03:29:29 2013 -0500
@@ -1,6 +1,7 @@
-<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0">
+<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.2">
     <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -116,7 +117,7 @@
       <when value="reference-point">
         <param name="referencePoint" type="select" label="The reference point for the plotting">
             <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
-            <option value="TES">end of region (e.g. TES)</option>
+            <option	 value="TES">end of region (e.g. TES)</option>
             <option value="center">center of region</option>
         </param>
         
@@ -126,19 +127,8 @@
         <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
       </when>
     </conditional>
-    
-    <conditional name="output" >
-        <param name="showOutputSettings" type="select" label="Show additional output options" >
-            <option value="no" selected="true">no</option>
-            <option value="yes">yes</option>
-        </param>
-          <when value="no" />
-          <when value="yes">
-            <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/>
-            <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/>
-            <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
-        </when>
-    </conditional>
+
+    <expand macro="graphic_output_settings" />
 
     <conditional name="advancedOpt" >
       <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -183,32 +173,8 @@
     
     </inputs>
   <outputs>
-    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix">
-    </data>
-    <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
-        <filter>
-        ((
-            output['showOutputSettings'] == 'yes' and 
-            output['saveData'] is True
-        ))
-        </filter>
-    </data>
-    <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
-        <filter>
-        ((
-            output['showOutputSettings'] == 'yes' and 
-            output['saveMatrix'] is True
-        ))
-        </filter>
-    </data>
-    <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
-        <filter>
-        ((
-            output['showOutputSettings'] == 'yes' and 
-            output['saveSortedRegions'] is True
-        ))
-        </filter>
-    </data>
+    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
+    <expand macro="output_graphic_outputs" />
   </outputs>
     <!--
     computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1