Mercurial > repos > mvdbeek > r_goseq_1_22_0
changeset 12:02e88556ce1d draft
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 06:44:44 -0500 |
| parents | 1802ccf465b8 |
| children | ea84562a5115 |
| files | get_length_and_gc_content.r tool_dependencies.xml |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- 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
--- 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>