Mercurial > repos > artbio > probecoverage
changeset 3:4f744d3aaf0b draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 8159fa0b4667a953c05aca50d412c33e619b5080
| author | artbio |
|---|---|
| date | Sun, 24 Sep 2017 14:47:11 -0400 |
| parents | 35d2db3753d9 |
| children | daec4df60281 |
| files | probecoverage.r probecoverage.xml test-data/graph_pysam.pdf |
| diffstat | 3 files changed, 8 insertions(+), 3 deletions(-) [+] |
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--- a/probecoverage.r Sun Sep 24 13:34:16 2017 -0400 +++ b/probecoverage.r Sun Sep 24 14:47:11 2017 -0400 @@ -12,6 +12,7 @@ make_option("--xlab", type = "character", help="X-axis legend"), make_option("--ylab", type = "character", help="Y-axis legend"), make_option("--sample", type = "character", help="a space separated of sample labels"), + make_option("--method", type = "character", help="bedtools or pysam"), make_option(c("-o", "--output"), type = "character", help="path to the pdf plot") ) @@ -30,8 +31,11 @@ } ## function - -cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome) +if (args$method == 'bedtools') { + cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome) + } else { + cumul <- function(x,y) sum(Table[,y] > x)/length(Table$chromosome) + } scaleFUN <- function(x) sprintf("%.3f", x) ## end of function
--- a/probecoverage.xml Sun Sep 24 13:34:16 2017 -0400 +++ b/probecoverage.xml Sun Sep 24 14:47:11 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="probecoverage" name="Probe Coverage" version="0.3.0"> +<tool id="probecoverage" name="Probe Coverage" version="0.4.0"> <description></description> <requirements> <requirement type="package" version="1.4.1">samtools</requirement> @@ -26,6 +26,7 @@ #end for -bed '$bed' > $coverage_dataframe && Rscript '$__tool_directory__'/probecoverage.r + --method '$method' --input '$coverage_dataframe' --title 'Probe coverage depth (cumulative distribution)' --xlab