# HG changeset patch
# User mvdbeek
# Date 1456399127 18000
# Node ID 7f8d888e335551bda81e087b43b6c5896337618b
# Parent  d1eed994287a0bc11263d5578e376df7148d347c
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty

diff -r d1eed994287a -r 7f8d888e3355 get_length_and_gc_content.r
--- a/get_length_and_gc_content.r	Thu Feb 25 06:16:23 2016 -0500
+++ b/get_length_and_gc_content.r	Thu Feb 25 06:18:47 2016 -0500
@@ -17,7 +17,7 @@
 
 GTFfile = args$gtf
 FASTAfile = args$fasta
-output = args$output
+output_file = args$output
 
 #Load the annotation and reduce it
 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon")
@@ -42,4 +42,4 @@
 output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
 colnames(output) <- c("Length", "GC")
 
-write.table(output, file="GC_lengths.tsv", sep="\t")
\ No newline at end of file
+write.table(output, file=output_file, sep="\t")
\ No newline at end of file