view corr.xml @ 14:5a4cbfb5fbc5 default tip

loading R3.0.2
author Ido Tamir <ido.tamir@imp.ac.at>
date Mon, 27 Oct 2014 10:57:35 +0100
parents de452b96da8e
children
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<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="optional name for condition, default: data name"/>
    </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, bam 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
   </help> 
</tool>