Mercurial > repos > iuc > annotatemyids
comparison test-data/out_rscript.txt @ 0:af97bb1b9435 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 46271ad3015ee41a825860084b2ab9d8081ecab8
| author | iuc |
|---|---|
| date | Wed, 03 Jan 2018 15:24:55 -0500 |
| parents | |
| children | 344471c33167 |
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| -1:000000000000 | 0:af97bb1b9435 |
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| 1 | |
| 2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
| 3 | |
| 4 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
| 5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
| 6 | |
| 7 id_type <- "ENSEMBL" | |
| 8 organism <- "Hs" | |
| 9 output_cols <- "ENSEMBL,ENTREZID,SYMBOL,GENENAME" | |
| 10 file_has_header <- FALSE | |
| 11 | |
| 12 ids <- as.character(read.table("/tmp/tmpY5XREO/files/000/dataset_3.dat", header=file_has_header)[,1]) | |
| 13 | |
| 14 if(organism == "Hs"){ | |
| 15 suppressPackageStartupMessages(library(org.Hs.eg.db)) | |
| 16 db <- org.Hs.eg.db | |
| 17 } else if (organism == "Mm"){ | |
| 18 suppressPackageStartupMessages(library(org.Mm.eg.db)) | |
| 19 db <- org.Mm.eg.db | |
| 20 } else if (organism == "Dm"){ | |
| 21 suppressPackageStartupMessages(library(org.Dm.eg.db)) | |
| 22 db <- org.Dm.eg.db | |
| 23 } else if (organism == "Dr"){ | |
| 24 suppressPackageStartupMessages(library(org.Dr.eg.db)) | |
| 25 db <- org.Dr.eg.db | |
| 26 } else { | |
| 27 cat(paste("Organism type not supported", organism)) | |
| 28 } | |
| 29 | |
| 30 cols <- unlist(strsplit(output_cols, ",")) | |
| 31 result <- select(db, keys=ids, keytype=id_type, columns=cols) | |
| 32 write.table(result, file="/tmp/tmpY5XREO/files/000/dataset_4.dat", sep="\t", row.names=FALSE, quote=FALSE) | |
| 33 | |
| 34 |