# HG changeset patch
# User mvdbeek
# Date 1456400684 18000
# Node ID 02e88556ce1d6c9af033e6fdfc505867026832b8
# Parent  1802ccf465b8b3d75d18699e3c689c0994f636a1
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty

diff -r 1802ccf465b8 -r 02e88556ce1d get_length_and_gc_content.r
--- a/get_length_and_gc_content.r	Thu Feb 25 06:20:59 2016 -0500
+++ b/get_length_and_gc_content.r	Thu Feb 25 06:44:44 2016 -0500
@@ -5,6 +5,7 @@
 library(rtracklayer)
 library(Rsamtools)
 library(optparse)
+library(data.table)
 
 option_list <- list(
     make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."),
@@ -40,6 +41,7 @@
     c(width, nGCs/width)
 }
 output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
-colnames(output) <- c("Length", "GC")
+output <- setDT(output, keep.rownames = TRUE)[]
+colnames(output) <- c("#gene_id", "length", "GC")
 
-write.table(output, file=output_file, sep="\t")
\ No newline at end of file
+write.table(output, file=output_file, row.names=FALSE, quote=FALSE, sep="\t")
\ No newline at end of file
diff -r 1802ccf465b8 -r 02e88556ce1d tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Feb 25 06:20:59 2016 -0500
+++ b/tool_dependencies.xml	Thu Feb 25 06:44:44 2016 -0500
@@ -4,6 +4,6 @@
          <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="goseq" version="1.22.0">
-         <repository changeset_revision="0552aea78457" name="package_r_3_2_1_goseq_1_22_0" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />
+         <repository changeset_revision="3b7064c31073" name="package_r_3_2_1_goseq_1_22_0" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>