Mercurial > repos > iuc > annotatemyids

comparison annotateMyIDs.xml @ 6:a4745bc5a840 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit a0c51ab52c4e3f296d5577ee3af26c4c1465e1e9
author iuc
date Fri, 08 Mar 2019 04:39:10 -0500
parents e7a359b56538
children f23e8ea9dd8a
comparison
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5:e7a359b56538 6:a4745bc5a840
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"){