view bigWigSummary.xml @ 16:0c3429d2dd4f 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>

    <tests>
	<test>
	    <param name="input" value="1.bigwig" />
	    <param name="chrom" value="chr21" />
	    <param name="start" value="10000000" />
            <param name="end" value="50000000" />
	    <param name="dataPoints" value="3" />
	    <param name="type" value="std" />
	    <output name="output" file="1.txt" />
	</test>
    </tests>
    <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>