view bigWigSummary.xml @ 6:558f7f9baa78 draft

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<tool id="bigWigSummary" name="bigWigSummary">
  <description> Extract summary information from a bigWig file. </description>
  <command> 
	bigWigSummary $input $chrom $start $end $dataPoints -type=$type> $output
  </command>
  <inputs>
    <param name="input" type="data" format="bigwig" label="Input"/>
    <param name="chrom" type="text" value="chr" label="Chromosome" help="E.g. 'chr7'"/>
    <param name="start" type="integer" value="" label="Start coordinate" help="BED format (0-based)."/>
    <param name="end" type="integer" value="" label="End coordinate" help="BED format (0-based)."/>    
      
    <param name="dataPoints" type="integer" value="1" label="Number of (equal) parts to break down the selected region."  help="Choose 1 for simple summary."/>
    <param name="type" type="select" label="Operation">
	<option value="mean">Average value in region (default)</option>
        <option value="min">Minimum value in region</option>
        <option value="max">Maximum value in region</option>
        <option value="std">Standard deviation in region</option>
        <option value="coverage">Percentage of region that is covered</option>
    </param>
  </inputs>
  
  <outputs>
    <data format="text" name="output"/> 
  </outputs>
  <help>

**Usage**
  * bigWigSummary file.bigWig chrom start end dataPoints
  * Get summary data from bigWig for indicated region, broken into dataPoints equal parts.  (Use dataPoints=1 for simple summary.)

  </help>
</tool>