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comparison dexseq.R @ 10:df929f257179 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 08:25:51 +0000
parents 62adf13b86ea
children 9a7c5b6d8f1e
comparison
equal deleted inserted replaced
9:b47c006d90c5 10:df929f257179
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({
25 "reportdir", "r", 1, "character", 26 "reportdir", "r", 1, "character",
26 "rds", "d", 1, "character", 27 "rds", "d", 1, "character",
27 "factors", "f", 1, "character", 28 "factors", "f", 1, "character",
28 "threads", "p", 1, "integer", 29 "threads", "p", 1, "integer",
29 "fdr", "c", 1, "double" 30 "fdr", "c", 1, "double"
30 ), byrow = TRUE, ncol = 4); 31 ), byrow = TRUE, ncol = 4)
31 opt <- getopt(spec); 32 opt <- getopt(spec)
32 33
33 # if help was asked for print a friendly message 34 # if help was asked for print a friendly message
34 # and exit with a non-zero error code 35 # and exit with a non-zero error code
35 if (!is.null(opt$help)) { 36 if (!is.null(opt$help)) {
36 cat(getopt(spec, usage = TRUE)); 37 cat(getopt(spec, usage = TRUE))
37 q(status = 1); 38 q(status = 1)
38 } 39 }
39 40
40 trim <- function(x) gsub("^\\s+|\\s+$", "", x) 41 trim <- function(x) gsub("^\\s+|\\s+$", "", x)
41 opt$samples <- trim(opt$samples) 42 opt$samples <- trim(opt$samples)
42 opt$factors <- trim(opt$factors) 43 opt$factors <- trim(opt$factors)
108 export_table <- as.data.frame(res_sorted) 109 export_table <- as.data.frame(res_sorted)
109 last_column <- ncol(export_table) 110 last_column <- ncol(export_table)
110 for (i in seq_len(nrow(export_table))) { 111 for (i in seq_len(nrow(export_table))) {
111 export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ") 112 export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ")
112 } 113 }
113 write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, col.names = FALSE) 114 export_table[, c(last_column)] <- sapply(export_table[, c(last_column)], as.character)
115 write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
114 print("Written Results") 116 print("Written Results")
115 117
116 if (!is.null(opt$rds)) { 118 if (!is.null(opt$rds)) {
117 saveRDS(res, file = "DEXSeqResults.rds") 119 saveRDS(res, file = "DEXSeqResults.rds")
118 } 120 }