Mercurial > repos > iuc > deseq2

diff get_deseq_dataset.R @ 35:03ad446aab5a 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 06:23:43 -0400
parents 13f324f9cdb7
children 951876579237
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line diff
--- a/get_deseq_dataset.R	Mon Feb 04 16:44:40 2019 -0500
+++ b/get_deseq_dataset.R	Tue Mar 26 06:23:43 2019 -0400
@@ -10,11 +10,11 @@
 
   if (!is.null(tximport)) {
     if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport")
-    if (tolower(file_ext(opt$tx2gene)) == "gff") {
+    if (tolower(file_ext(tx2gene)) == "gff") {
       gffFile <-tx2gene
     } else {
       gffFile <- NULL
-      tx2gene <- read.table(tx2gene, header=FALSE)
+      tx2gene <- read.table(tx2gene, header=hasHeader)
     }
     useTXI <- TRUE
   } else {