Mercurial > repos > rnateam > chipseeker
changeset 4:90fe78a19b55 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 6f594126ac7369cc80c30a02a6df57e785dfb45a
| author | rnateam |
|---|---|
| date | Mon, 26 Nov 2018 06:21:37 -0500 |
| parents | 535321abf9a4 |
| children | 4c2dbe4dbb4e |
| files | chipseeker.R chipseeker.xml |
| diffstat | 2 files changed, 11 insertions(+), 10 deletions(-) [+] |
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--- a/chipseeker.R Fri Jun 01 02:13:33 2018 -0400 +++ b/chipseeker.R Mon Nov 26 06:21:37 2018 -0500 @@ -53,17 +53,18 @@ # Convert from 1-based to 0-based format if (format == "interval") { metacols <- apply(as.data.frame(metacols), 1, function(col) paste(col, collapse="|")) - resout <- data.frame(Chrom=res$seqnames, - Start=res$start - 1, - End=res$end, - Comment=metacols) + resout <- data.frame(res$seqnames, + res$start - 1, + res$end, + metacols) + colnames(resout)[1:4] <- c("Chrom", "Start", "End", "Comment") } else { - resout <- data.frame(Chrom=res$seqnames, - Start=res$start - 1, - End=res$end, + resout <- data.frame(res$seqnames, + res$start - 1, + res$end, metacols) + colnames(resout)[1:3] <- c("Chrom", "Start", "End") } - write.table(resout, file="out.tab", sep="\t", row.names=FALSE, quote=FALSE) if (!is.null(args$plots)) {
--- a/chipseeker.xml Fri Jun 01 02:13:33 2018 -0400 +++ b/chipseeker.xml Mon Nov 26 06:21:37 2018 -0500 @@ -1,7 +1,7 @@ -<tool id="chipseeker" name="ChIPseeker" version="1.14.2.2"> +<tool id="chipseeker" name="ChIPseeker" version="1.16.1"> <description>for ChIP peak annotation and visualization</description> <requirements> - <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement> + <requirement type="package" version="1.16.1">bioconductor-chipseeker</requirement> <requirement type="package" version="1.4.4">r-optparse</requirement> </requirements> <version_command><![CDATA[