Mercurial > repos > iuc > annotatemyids
comparison annotateMyIDs.xml @ 6:ecc913a7334b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a0c51ab52c4e3f296d5577ee3af26c4c1465e1e9
author | iuc |
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date | Fri, 08 Mar 2019 04:39:31 -0500 |
parents | b467a89be0c6 |
children | 1aae04680c4b |
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5:b467a89be0c6 | 6:ecc913a7334b |
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27 organism <- "${organism}" | 27 organism <- "${organism}" |
28 output_cols <- "${output_cols}" | 28 output_cols <- "${output_cols}" |
29 file_has_header <- ${file_has_header} | 29 file_has_header <- ${file_has_header} |
30 remove_dups <- ${remove_dups} | 30 remove_dups <- ${remove_dups} |
31 | 31 |
32 ids <- as.character(read.table('$id_file', header=file_has_header)[,1], sep="\t", quote="") | 32 input <- read.table('$id_file', header=file_has_header, sep="\t", quote="") |
33 ids <- as.character(input[, 1]) | |
33 | 34 |
34 if(organism == "Hs"){ | 35 if(organism == "Hs"){ |
35 suppressPackageStartupMessages(library(org.Hs.eg.db)) | 36 suppressPackageStartupMessages(library(org.Hs.eg.db)) |
36 db <- org.Hs.eg.db | 37 db <- org.Hs.eg.db |
37 } else if (organism == "Mm"){ | 38 } else if (organism == "Mm"){ |