Mercurial > repos > geert-vandeweyer > coverage_report
comparison CoverageReport.xml @ 23:a718420c834e draft
Added (default) option to collapse repetitive BED files.
| author | geert-vandeweyer |
|---|---|
| date | Thu, 12 Feb 2015 08:51:06 -0500 |
| parents | b8e4ed167120 |
| children |
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| 22:95062840f80f | 23:a718420c834e |
|---|---|
| 14 ## run parameters | 14 ## run parameters |
| 15 $perGene | 15 $perGene |
| 16 $PositionLevel | 16 $PositionLevel |
| 17 -m $threshold | 17 -m $threshold |
| 18 -f $frac | 18 -f $frac |
| 19 $trim | |
| 19 ## sample name | 20 ## sample name |
| 20 #if $namefromselect.namesource == "typed" : | 21 #if $namefromselect.namesource == "typed" : |
| 21 -n "${namefromselect.typedname}" | 22 -n "${namefromselect.typedname}" |
| 22 #elif $namefromselect.namesource == "other": | 23 #elif $namefromselect.namesource == "other": |
| 23 -n "${namefromselect.namefile.display_name}" | 24 -n "${namefromselect.namefile.display_name}" |
| 24 #elif $namefromselect.namesource == "bam": | 25 #elif $namefromselect.namesource == "bam": |
| 25 -n "${input1.display_name}" | 26 -n "${input1.display_name}" |
| 26 #else: | 27 #else: |
| 27 -n "Unspecified" | 28 -n "Unspecified" |
| 28 #end if | 29 #end if |
| 30 | |
| 29 </command> | 31 </command> |
| 30 <requirements> | 32 <requirements> |
| 31 <requirement type="package" version="3.0.3">R</requirement> | 33 <requirement type="package" version="3.0.3">R</requirement> |
| 32 <requirement type="package" version="2.18.2">bedtools</requirement> | 34 <requirement type="package" version="2.18.2">bedtools</requirement> |
| 33 <requirement type="package" version="0.1.18">samtools</requirement> | 35 <requirement type="package" version="0.1.18">samtools</requirement> |
| 34 </requirements> | 36 </requirements> |
| 35 <inputs> | 37 <inputs> |
| 36 <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" /> | 38 <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" /> |
| 37 <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" /> | 39 <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" /> |
| 40 <param name="trim" type="select" label="Collapse overlapping regions in targets"> | |
| 41 <option value='-T' selected="TRUE">Yes</option> | |
| 42 <option value=''>No</option> | |
| 43 </param> | |
| 38 <param name="threshold" type="integer" value="40" label="Minimal Coverage Threshold" help="Default: 40" /> | 44 <param name="threshold" type="integer" value="40" label="Minimal Coverage Threshold" help="Default: 40" /> |
| 39 <param name="frac" type="float" value="0.2" label="Fraction of Average Coverage for usage in plot" help="Default: 0.2" /> | 45 <param name="frac" type="float" value="0.2" label="Fraction of Average Coverage for usage in plot" help="Default: 0.2" /> |
| 40 <param name="perGene" type="select" label="Plot exon coverages for all genes in targets"> | 46 <param name="perGene" type="select" label="Plot exon coverages for all genes in targets"> |
| 41 <option value='-r'>Yes</option> | 47 <option value='-r'>Yes</option> |
| 42 <option value=''>No</option> | 48 <option value=''>No</option> |