Mercurial > repos > iuc > annotatemyids
comparison test-data/out_rscript.txt @ 11:4f2967b27e67 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids commit 3e791f5bd978eee4cd42787c33d4cccc76612c9e
author | iuc |
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date | Fri, 01 Jul 2022 12:24:49 +0000 |
parents | 442e2d79b05c |
children |
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10:f29602ae449e | 11:4f2967b27e67 |
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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 |