diff profiler.xml @ 22:8710187d1eb5 draft

Uploaded

--- a/profiler.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/profiler.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -3,6 +3,7 @@
         creates a profile plot for a score associated to genomic regions
     </description>
     <expand macro="requirements" />
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -80,7 +81,9 @@
             </when>
         </conditional>
 
-        <expand macro="graphic_output_settings" />
+        <expand macro="graphic_output_settings">
+            <expand macro="image_file_format" />
+        <expand>
 
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -130,17 +133,9 @@
                 <when input="output.outFileFormat" value="emf" format="emf" />
             </change_format>
         </data>
-        <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
-            <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
-        </data>
-        <data format="tabular" name="outFileNameMatrix" label="${tool.name} matrix of heatmap values">
-            <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
-        </data>
-        <data format="bed" name="outFileSortedRegions" label="${tool.name} sorted/filtered regions">
-            <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
-        </data>
-  </outputs>
-  <help>
+        <expand macro="output_graphic_outputs" />
+    </outputs>
+    <help>
 
 **What it does**