Mercurial > repos > iuc > deseq2

comparison get_deseq_dataset.R @ 23:0696db066a5b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2
author iuc
date Tue, 26 Mar 2019 06:25:00 -0400
parents 89d26b11d452
children de44f8eff84a
comparison
equal deleted inserted replaced
22:e5c8afac22a7 23:0696db066a5b
8 hasHeader <- FALSE 8 hasHeader <- FALSE
9 } 9 }
10 10
11 if (!is.null(tximport)) { 11 if (!is.null(tximport)) {
12 if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport") 12 if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport")
13 if (tolower(file_ext(opt$tx2gene)) == "gff") { 13 if (tolower(file_ext(tx2gene)) == "gff") {
14 gffFile <-tx2gene 14 gffFile <-tx2gene
15 } else { 15 } else {
16 gffFile <- NULL 16 gffFile <- NULL
17 tx2gene <- read.table(tx2gene, header=FALSE) 17 tx2gene <- read.table(tx2gene, header=hasHeader)
18 } 18 }
19 useTXI <- TRUE 19 useTXI <- TRUE
20 } else { 20 } else {
21 useTXI <- FALSE 21 useTXI <- FALSE
22 } 22 }