Mercurial > repos > iuc > dexseq

comparison plotdexseq.R @ 17:d104044e4257 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
author iuc
date Tue, 04 Apr 2023 08:25:36 +0000
parents 3762d6644ec4
children ffa256d657b2
comparison
equal deleted inserted replaced
16:661f29c77bb0 17:d104044e4257
1 ## Setup R error handling to go to stderr 1 ## Setup R error handling to go to stderr
2 options(show.error.messages = F, error = function() { 2 options(show.error.messages = FALSE, error = function() {
3 cat(geterrmessage(), file = stderr()); q("no", 1, F) 3 cat(geterrmessage(), file = stderr())
4 q("no", 1, FALSE)
4 }) 5 })
5 # we need that to not crash galaxy with an UTF8 error on German LC settings. 6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
6 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") 7 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
7 8
8 suppressPackageStartupMessages({ 9 suppressPackageStartupMessages({
23 "fdr", "c", 1, "double", 24 "fdr", "c", 1, "double",
24 "transcripts", "t", 1, "logical", 25 "transcripts", "t", 1, "logical",
25 "names", "a", 1, "logical", 26 "names", "a", 1, "logical",
26 "normcounts", "n", 1, "logical", 27 "normcounts", "n", 1, "logical",
27 "splicing", "s", 1, "logical" 28 "splicing", "s", 1, "logical"
28 ), byrow = TRUE, ncol = 4); 29 ), byrow = TRUE, ncol = 4)
29 opt <- getopt(spec); 30 opt <- getopt(spec)
30 31
31 res <- readRDS(opt$rdata) 32 res <- readRDS(opt$rdata)
32 33
33 if (!is.null(opt$genefile)) { 34 if (!is.null(opt$genefile)) {
34 genes <- read.delim(opt$genefile, header = FALSE) 35 genes <- read.delim(opt$genefile, header = FALSE)