Mercurial > repos > kpbioteam > chipeakanno_annopeaks
changeset 9:8d05c398fecd draft
planemo upload for repository https://github.com/kpbioteam/chipeakanno_annopeaks commit 5ee10ba73cd634a41b84f059f02edeaa04f69b8d-dirty
| author | kpbioteam |
|---|---|
| date | Thu, 21 Jun 2018 11:38:08 -0400 |
| parents | 0473a72c943c |
| children | b1274d30071e |
| files | chipeakanno_annopeaks.R chipeakanno_annopeaks.xml |
| diffstat | 2 files changed, 4 insertions(+), 1 deletions(-) [+] |
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--- a/chipeakanno_annopeaks.R Thu Jun 21 11:21:03 2018 -0400 +++ b/chipeakanno_annopeaks.R Thu Jun 21 11:38:08 2018 -0400 @@ -11,12 +11,13 @@ input2 = args[2] input3 = as.numeric(args[3]) input4 = as.numeric(args[4]) +input5 = as.numeric(args[5]) output1 = args[5] DMRInfo <- read.table(input1) peaks <- GRanges(seqnames = DMRInfo[, 1], ranges = IRanges - (start = DMRInfo[, 2], end = DMRInfo[, 3]),score=DMRInfo[, 9]) + (start = DMRInfo[, 2], end = DMRInfo[, 3]),score=DMRInfo[, input5]) annoData <- toGRanges(EnsDb.Hsapiens.v75) seqlevelsStyle(peaks) <- seqlevelsStyle(annoData)
--- a/chipeakanno_annopeaks.xml Thu Jun 21 11:21:03 2018 -0400 +++ b/chipeakanno_annopeaks.xml Thu Jun 21 11:38:08 2018 -0400 @@ -18,6 +18,8 @@ </param> <param name="input3" type="text" value="-5000" label="bindingRegionStart" help="e.g. to obtain peaks within 5kb upstream and up to 3kb downstream of TSS within the gene body, set bindingType = startSite and bindingRegion = c(-5000, 3000)"/> <param name="input4" type="text" value="3000" label="bindingRegionEnd" help="e.g. to obtain peaks with nearest bi-directional promoters within 5kb upstream and 3kb downstream of TSS, set bindingType = nearestBiDirectionalPromoters and bindingRegion = c(-5000, 3000)"/> + +<param name="input5" type="text" value="1" label="Additional Column of Score" help="Position of Additional Column of the Score" /> </inputs> <outputs> <data name="output1" format="txt" />