Mercurial > repos > iuc > deseq2
changeset 21:a6fc9228e1a0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3
| author | iuc |
|---|---|
| date | Mon, 28 Jan 2019 12:04:08 -0500 |
| parents | 89d26b11d452 |
| children | e5c8afac22a7 |
| files | deseq2.R deseq2.xml |
| diffstat | 2 files changed, 13 insertions(+), 3 deletions(-) [+] |
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--- a/deseq2.R Thu Dec 06 15:49:22 2018 -0500 +++ b/deseq2.R Mon Jan 28 12:04:08 2019 -0500 @@ -46,7 +46,8 @@ spec <- matrix(c( "quiet", "q", 0, "logical", "help", "h", 0, "logical", - "batch_factors", "", 1, "character", + "cores", "s", 0, "integer", + "batch_factors", "w", 1, "character", "outfile", "o", 1, "character", "countsfile", "n", 1, "character", "rlogfile", "r", 1, "character", @@ -105,6 +106,14 @@ library("gplots") }) +if (opt$cores > 1) { + library("BiocParallel") + register(MulticoreParam(opt$cores)) + parallel = TRUE +} else { + parallel = FALSE +} + # build or read sample table trim <- function (x) gsub("^\\s+|\\s+$", "", x) @@ -273,7 +282,7 @@ if (verbose) cat(paste("using disperion fit type:",fitType,"\n")) # run the analysis -dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep) +dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep, parallel=parallel) # create the generic plots and leave the device open if (!is.null(opt$plots)) {
--- a/deseq2.xml Thu Dec 06 15:49:22 2018 -0500 +++ b/deseq2.xml Mon Jan 28 12:04:08 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="deseq2" name="DESeq2" version="2.11.40.4"> +<tool id="deseq2" name="DESeq2" version="2.11.40.5"> <description>Determines differentially expressed features from count tables</description> <requirements> <requirement type="package" version="1.20.0">bioconductor-deseq2</requirement> @@ -41,6 +41,7 @@ #import json #import os Rscript '${__tool_directory__}/deseq2.R' + --cores \${GALAXY_SLOTS:-1} -o '$deseq_out' #if $pdf: -p '$plots'