<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.

Please turn to *Ido Tamir* in case of problems or suggestions for this tool.

TODO:
-----
-    Add mappability track option
-    Add bam as input
   </help> 
</tool>