Mercurial > repos > geert-vandeweyer > coverage_report
changeset 23:a718420c834e draft
Added (default) option to collapse repetitive BED files.
| author | geert-vandeweyer |
|---|---|
| date | Thu, 12 Feb 2015 08:51:06 -0500 |
| parents | 95062840f80f |
| children | fd788f9db899 |
| files | CoverageReport.xml |
| diffstat | 1 files changed, 6 insertions(+), 0 deletions(-) [+] |
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--- a/CoverageReport.xml Mon Nov 17 07:10:11 2014 -0500 +++ b/CoverageReport.xml Thu Feb 12 08:51:06 2015 -0500 @@ -16,6 +16,7 @@ $PositionLevel -m $threshold -f $frac + $trim ## sample name #if $namefromselect.namesource == "typed" : -n "${namefromselect.typedname}" @@ -26,6 +27,7 @@ #else: -n "Unspecified" #end if + </command> <requirements> <requirement type="package" version="3.0.3">R</requirement> @@ -35,6 +37,10 @@ <inputs> <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" /> <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" /> + <param name="trim" type="select" label="Collapse overlapping regions in targets"> + <option value='-T' selected="TRUE">Yes</option> + <option value=''>No</option> + </param> <param name="threshold" type="integer" value="40" label="Minimal Coverage Threshold" help="Default: 40" /> <param name="frac" type="float" value="0.2" label="Fraction of Average Coverage for usage in plot" help="Default: 0.2" /> <param name="perGene" type="select" label="Plot exon coverages for all genes in targets">