diff heatmapper.xml @ 22:8710187d1eb5 draft

Uploaded

--- a/heatmapper.xml	Tue Dec 10 11:03:36 2013 -0500
+++ b/heatmapper.xml	Thu Dec 12 18:11:46 2013 -0500
@@ -1,10 +1,7 @@
 <tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
     <description>creates a heatmap for a score associated to genomic regions</description>
-    <expand macro="requirements">
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="1.2.1">matplotlib</requirement>
-        <requirement type="package" version="0.12.0">scipy</requirement>
-    </expand>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
@@ -89,7 +86,9 @@
   <inputs>
     <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
 
-    <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" >
@@ -162,22 +161,16 @@
   </inputs>
   <outputs>
     <data format="png" name="outFileName" label="${tool.name} image">
-    <change_format>
-        <when input="output.outFileFormat" value="pdf" format="pdf" />
-        <when input="output.outFileFormat" value="svg" format="svg" />
-        <when input="output.outFileFormat" value="eps" format="eps" />
-        <when input="output.outFileFormat" value="emf" format="emf" />
-    </change_format>
+        <change_format>
+            <when input="output.outFileFormat" value="pdf" format="pdf" />
+            <when input="output.outFileFormat" value="svg" format="svg" />
+            <when input="output.outFileFormat" value="eps" format="eps" />
+            <when input="output.outFileFormat" value="emf" format="emf" />
+        </change_format>
     </data>
-    <data format="tabular" name="outFileNameData" label="${tool.name} 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>  
+
+    <expand macro="output_graphic_outputs" />
+
   </outputs>
     <tests>
         <test>