--- a/deepTools_macros.xml	Tue Dec 10 12:13:18 2013 -0500
+++ b/deepTools_macros.xml	Sat Dec 14 03:29:29 2013 -0500
@@ -43,17 +43,27 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement>
+            <requirement type="package" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
+            <requirement type="package" version="0.12.0">scipy</requirement>
             <requirement type="package" version="1.2.1">matplotlib</requirement>
             <requirement type="package" version="0.1.19">samtools</requirement>
             <requirement type="package" version="12-2013">bx-python</requirement>
             <yield />
         </requirements>
-        </macro>
-
+    </macro>
+    <macro name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+            <exit_code range="0" level="warning" description="Warning" />
+            <regex match="Error:" />
+            <regex match="Exception:" />
+            <regex match="EXception:" />
+        </stdio>
+    </macro>
     <token name="@REFERENCES@">
 
 For more informations, please visit our `project site`_.
@@ -144,6 +154,16 @@
         </conditional>
     </macro>
 
+    <macro name="image_file_format">
+        <param name="outFileFormat" type="select" label="Image file format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="eps">eps</option>
+            <option value="emf">emf</option>
+        </param>
+    </macro>
+
     <macro name="graphic_output_settings">
         <conditional name="output" >
             <param name="showOutputSettings" type="select" label="Show advanced output settings" >
@@ -166,8 +186,42 @@
         </conditional>
     </macro>
 
+    <macro name="output_graphic_outputs">
+        <data format="png" name="outFileName" label="${tool.name} image">
+            <change_format>
+                <when input="output.outFileFormat" value="pdf" format="pdf" />
+                <when input="output.outFileFormat" value="svg" format="svg" />
+                <when input="output.outFileFormat" value="eps" format="eps" />
+                <when input="output.outFileFormat" value="emf" format="emf" />
+            </change_format>
+        </data>
+        <data format="tabular" name="outFileNameData" label="${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>
+    </macro>
+
     <macro name="colormap">
-
         <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
             <option value="RdYlBu" selected="true">RdYlBu</option>
             <option value="Accent">Accent</option>