Mercurial > repos > nikos > ucsc_tools
changeset 5:998c98233c36 draft
Uploaded
| author | nikos |
|---|---|
| date | Tue, 15 Jul 2014 07:19:39 -0400 |
| parents | 5b5460b79488 |
| children | 558f7f9baa78 |
| files | bigWigSummary.xml |
| diffstat | 1 files changed, 33 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigWigSummary.xml Tue Jul 15 07:19:39 2014 -0400 @@ -0,0 +1,33 @@ +<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> +