comparison dexseq.R @ 18:ffa256d657b2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598

17:d104044e4257

options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
args <- commandArgs(trailingOnly = TRUE)

#get options, using the spec as defined by the enclosed list.
#we read the options from the default: commandArgs(TRUE).
spec <- matrix(c(
    "verbose", "v", 2, "integer",
    "help", "h", 0, "logical",
    "gtf", "a", 1, "character",
    "outfile", "o", 1, "character",

head(res_sorted)

export_table <- as.data.frame(res_sorted)
last_column <- ncol(export_table)
for (i in seq_len(nrow(export_table))) {
  export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ")
}
export_table[, c(last_column)] <- sapply(export_table[, c(last_column)], as.character)
write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
print("Written Results")

18:ffa256d657b2

options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
args <- commandArgs(trailingOnly = TRUE)

# get options, using the spec as defined by the enclosed list.
# we read the options from the default: commandArgs(TRUE).
spec <- matrix(c(
    "verbose", "v", 2, "integer",
    "help", "h", 0, "logical",
    "gtf", "a", 1, "character",
    "outfile", "o", 1, "character",

head(res_sorted)

export_table <- as.data.frame(res_sorted)
last_column <- ncol(export_table)
for (i in seq_len(nrow(export_table))) {
    export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ")
}
export_table[, c(last_column)] <- sapply(export_table[, c(last_column)], as.character)
write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
print("Written Results")