Mercurial > repos > mvdbeek > r_goseq_1_22_0
changeset 19:9442d1bf6d93 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
| author | mvdbeek |
|---|---|
| date | Fri, 26 Feb 2016 13:26:56 -0500 |
| parents | 5fb82111ec62 |
| children | |
| files | goseq.r goseq.xml |
| diffstat | 2 files changed, 5 insertions(+), 4 deletions(-) [+] |
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--- a/goseq.r Fri Feb 26 11:42:43 2016 -0500 +++ b/goseq.r Fri Feb 26 13:26:56 2016 -0500 @@ -13,7 +13,7 @@ make_option(c("-c", "--cutoff"), type="double",dest="p_adj_cutoff", help="Genes with p.adjust below cutoff are considered not differentially expressed and serve as control genes"), make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"), - make_option(c("-lf", "--length_file"), default=FALSE, help = "Path to "), + make_option(c("-lf", "--length_file"), type="character", default="FALSE", help = "Path to tabular file mapping gene id to length"), make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up correct gene length]"), make_option(c("-i", "--gene_id"), type="character", help="Gene ID of gene column in DGE file") ) @@ -40,8 +40,9 @@ names(genes) = dge_table[,1] # Assuming first row contains gene names # Get gene lengths -if (length_file !=FALSE) { - length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE, row.names=TRUE) +if (length_file != "FALSE" ) { + length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE) + row.names(length_table) = length_table[,1] gene_lengths = length_table[names(genes),]$length } else { gene_lengths = getlength(names(genes), genome, gene_id)
--- a/goseq.xml Fri Feb 26 11:42:43 2016 -0500 +++ b/goseq.xml Fri Feb 26 13:26:56 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="goseq" name="goseq gene ontology analyser" version="0.1.4"> +<tool id="goseq" name="goseq gene ontology analyser" version="0.1.5"> <description /> <requirements> <requirement type="package" version="3.2.1">R</requirement>