--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/corr.xml	Sun Aug 18 09:42:18 2013 -0400
@@ -0,0 +1,60 @@
+<tool id="corrcoverage" name="correlation" version="0.5.0">
+   <description>of coverage</description>
+   <command interpreter="sh">
+     mkCorr.sh
+     #echo ','.join(map(lambda (x): x.get('file').__str__(), $files))
+	 
+	 #echo ','.join(map(lambda (x): "\""+(x.get('file').name if x.get('cname').__str__() == "" else x.get('cname').__str__())+"\"", $files))
+	 
+	 #echo ','.join(map(lambda (x): x.get('file').ext, $files))
+	 
+	 $plotout
+
+	 $matout
+
+     "$name"
+   </command>
+  
+   <inputs>
+    <param name="name" type="text" label="experiment name" value="NA"></param>
+    <repeat name="files" title="input files" min="2">
+        <param name="file" format="bed,bigWig" type="data" label="file" help="input file for correlation"/>
+        <param name="cname" format="text" type="text" label="optional name" value="" help="name for condition"/>
+    </repeat>
+    
+   </inputs>
+
+   <outputs>
+	   <data format="pdf" name="plotout" label="#if str($name) == 'NA' then $on_string else $name# correlation plot"/> 
+	   <data format="tabular" name="matout" label="#if str($name) == 'NA' then $on_string else $name# correlation matrix"/>
+   </outputs>
+   
+   
+   <help>
+Correlate Coverage:
+===================
+
+Takes at least two files and calculates the correlation of the coverage. The correlation
+is calculated by using the union of all the regions that are covered in the tracks. 
+
+Requirements:
+-------------
+
+At least two files of 6 column bed, wig(?) or bigWig format 
+
+Outputs:
+--------
+Plot of pearson clustering of correlation coefficient.
+Matrix of pearson correlation coefficients.
+
+TODO:
+-----
+Add mappability track option
+Add bam as input
+   </help> 
+</tool>
+
+
+
+
+