Mercurial > repos > iuc > annotatemyids

comparison test-data/out_rscript.txt @ 11:4f2967b27e67 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
author iuc
date Fri, 01 Jul 2022 12:24:49 +0000
parents 442e2d79b05c
children
comparison
equal deleted inserted replaced
10:f29602ae449e 11:4f2967b27e67
6 6
7 id_type <- "ENSEMBL" 7 id_type <- "ENSEMBL"
8 organism <- "Hs" 8 organism <- "Hs"
9 output_cols <- "ENSEMBL,ENTREZID,SYMBOL,GENENAME" 9 output_cols <- "ENSEMBL,ENTREZID,SYMBOL,GENENAME"
10 file_has_header <- FALSE 10 file_has_header <- FALSE
11 remove_dups <- FALSE
11 12
12 ids <- as.character(read.table("/tmp/tmpY5XREO/files/000/dataset_3.dat", header=file_has_header)[,1]) 13 input <- read.table('/tmp/tmpqa0_mcvo/files/3/1/c/dataset_31cbce15-3708-4c78-bdf6-aca07697ccb7.dat', header=file_has_header, sep="\t", quote="")
14 ids <- as.character(input[, 1])
13 15
14 if(organism == "Hs"){ 16 if(organism == "Hs"){
15 suppressPackageStartupMessages(library(org.Hs.eg.db)) 17 suppressPackageStartupMessages(library(org.Hs.eg.db))
16 db <- org.Hs.eg.db 18 db <- org.Hs.eg.db
17 } else if (organism == "Mm"){ 19 } else if (organism == "Mm"){
21 suppressPackageStartupMessages(library(org.Dm.eg.db)) 23 suppressPackageStartupMessages(library(org.Dm.eg.db))
22 db <- org.Dm.eg.db 24 db <- org.Dm.eg.db
23 } else if (organism == "Dr"){ 25 } else if (organism == "Dr"){
24 suppressPackageStartupMessages(library(org.Dr.eg.db)) 26 suppressPackageStartupMessages(library(org.Dr.eg.db))
25 db <- org.Dr.eg.db 27 db <- org.Dr.eg.db
28 } else if (organism == "Rn"){
29 suppressPackageStartupMessages(library(org.Rn.eg.db))
30 db <- org.Rn.eg.db
31 } else if (organism == "At"){
32 suppressPackageStartupMessages(library(org.At.tair.db))
33 db <- org.At.tair.db
26 } else { 34 } else {
27 cat(paste("Organism type not supported", organism)) 35 cat(paste("Organism type not supported", organism))
28 } 36 }
29 37
30 cols <- unlist(strsplit(output_cols, ",")) 38 cols <- unlist(strsplit(output_cols, ","))
31 result <- select(db, keys=ids, keytype=id_type, columns=cols) 39 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) 40
41 if(remove_dups) {
42 result <- result[!duplicated(result$ENSEMBL),]
43 }
44
45 write.table(result, file='/tmp/tmpqa0_mcvo/job_working_directory/000/4/outputs/galaxy_dataset_b06fd1c6-69cb-4c43-9caf-1a445a3b8b2e.dat', sep="\t", row.names=FALSE, quote=FALSE)
33 46
34 47