# HG changeset patch
# User iuc
# Date 1553595900 14400
# Node ID 0696db066a5b9c7f0bdf47708a8f1da869fb3284
# Parent  e5c8afac22a79477b997b9ce04e90a140013654f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9ed3d83cc447ee897af867362bf1dd67af8a11c2

diff -r e5c8afac22a7 -r 0696db066a5b get_deseq_dataset.R
--- a/get_deseq_dataset.R	Mon Feb 04 16:45:12 2019 -0500
+++ b/get_deseq_dataset.R	Tue Mar 26 06:25:00 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 {