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<tool id="bed2rgb" name="Add different colors">
  <description>to different replicates</description>
  <command interpreter="perl">
                    /home/galaxy/tools/CTK/bed2rgb.pl -v -col $color $inputfile $outputfile
  </command>
  <inputs>
        <param name="inputfile" format="bed"  type="data" label="Input BED file" />
	<param name="color"  type="text" value="" label="Color by name or RGB (red; green; blue; ...; R,G,B; see help below for more information)" />
  </inputs>
  <outputs>
        <data name="outputfile" format="bed" label="Add RGB colors on ${on_string}">
        </data> 
  </outputs>

  <help>

.. class:: infomark

**What this tool does**

This tool will add different colors to BED files in RGB format. 

It will take as input files in BED format of unique CLIP tags and output files in BED format of RGB colored unique CLIP tags.

Repeat the step for all uniq.bed files to generate RGB-bed files, but use different RGB colors "x,x,x" (e.g. 128,0,0).
See http://www.rapidtables.com/web/color/RGB_Color.htm or other charts.

After getting the unique tags of each library, one might concatenate biological replicates for both BED files and mutation files, which are distinguished by different colors using this tool.

  </help>
</tool>