Mercurial > repos > mvdbeek > r_goseq_1_22_0

diff get_length_and_gc_content.r @ 10:7f8d888e3355 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Thu, 25 Feb 2016 06:18:47 -0500
parents 15ce6435ab83
children 02e88556ce1d
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line diff
--- 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