# HG changeset patch
# User mvdbeek
# Date 1456397348 18000
# Node ID d4b5942ed347e37e2600f4b0f873b68264b7c563
# Parent  f9b964d1d3860c50a8fb4a5610a3d77d118df05b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty

diff -r f9b964d1d386 -r d4b5942ed347 get_length_and_gc_content.r
--- a/get_length_and_gc_content.r	Thu Feb 25 05:47:38 2016 -0500
+++ b/get_length_and_gc_content.r	Thu Feb 25 05:49:08 2016 -0500
@@ -1,4 +1,5 @@
 # originally by Devon Ryan, https://www.biostars.org/p/84467/
+sink(stdout(), type = "message")
 
 library(GenomicRanges)
 library(rtracklayer)
@@ -19,7 +20,7 @@
 output = args$output
 
 #Load the annotation and reduce it
-GTF <- import.gff(GTFfile, format="gtf", genome=NA, asRangedData=F, feature.type="exon")
+GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon")
 grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name))
 reducedGTF <- unlist(grl, use.names=T)
 elementMetadata(reducedGTF)$gene_name <- rep(names(grl), elementLengths(grl))