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comparison dexseq.R @ 11:9a7c5b6d8f1e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
author iuc
date Tue, 02 Apr 2024 12:59:54 +0000
parents df929f257179
children
comparison
equal deleted inserted replaced
10:df929f257179 11:9a7c5b6d8f1e
14 14
15 15
16 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) 16 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
17 args <- commandArgs(trailingOnly = TRUE) 17 args <- commandArgs(trailingOnly = TRUE)
18 18
19 #get options, using the spec as defined by the enclosed list. 19 # get options, using the spec as defined by the enclosed list.
20 #we read the options from the default: commandArgs(TRUE). 20 # we read the options from the default: commandArgs(TRUE).
21 spec <- matrix(c( 21 spec <- matrix(c(
22 "verbose", "v", 2, "integer", 22 "verbose", "v", 2, "integer",
23 "help", "h", 0, "logical", 23 "help", "h", 0, "logical",
24 "gtf", "a", 1, "character", 24 "gtf", "a", 1, "character",
25 "outfile", "o", 1, "character", 25 "outfile", "o", 1, "character",
107 head(res_sorted) 107 head(res_sorted)
108 108
109 export_table <- as.data.frame(res_sorted) 109 export_table <- as.data.frame(res_sorted)
110 last_column <- ncol(export_table) 110 last_column <- ncol(export_table)
111 for (i in seq_len(nrow(export_table))) { 111 for (i in seq_len(nrow(export_table))) {
112 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 = ", ")
113 } 113 }
114 export_table[, c(last_column)] <- sapply(export_table[, c(last_column)], as.character) 114 export_table[, c(last_column)] <- sapply(export_table[, c(last_column)], as.character)
115 write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE) 115 write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
116 print("Written Results") 116 print("Written Results")
117 117