view tximport.R @ 3:0bcc35b10569 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e

# setup R error handling to go to stderr
options(show.error.messages = F, error = function() {
    cat(geterrmessage(), file = stderr())
    q("no", 1, F)
})

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("getopt")
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(
        "help", "h", 0, "logical",
        "out_file", "o", 1, "character",
        "countsFiles", "n", 1, "character",
        "countsFromAbundance", "r", 1, "character",
        "format", "v", 1, "character",
        "gff_file", "H", 0, "character",
        "tx2gene", "f", 0, "character",
        "geneIdCol", "l", 0, "character",
        "txIdCol", "p", 1, "character",
        "abundanceCol", "i", 0, "character",
        "countsCol", "y", 1, "character",
        "lengthCol", "x", 1, "character"
    ),
    byrow = TRUE, ncol = 4
)

opt <- getopt(spec)

# if help was asked for print a friendly message
# and exit with a non-zero error code
if (!is.null(opt$help)) {
    cat(getopt(spec, usage = TRUE))
    q(status = 1)
}

if (is.null(opt$gff_file) & is.null(opt$tx2gene)) {
    cat("A GFF/GTF file or a tx2gene table is required\n")
    q(status = 1)
}

if (opt$format == "none") { # custom format
    if (is.null(opt$txIdCol) | is.null(opt$abundanceCol) | is.null(opt$countsCol) | is.null(opt$lengthCol)) {
        cat("If you select a custom format for the input files you need to specify the column names\n")
        q(status = 1)
    }
}

if (is.null(opt$countsFiles)) {
    cat("'countsFiles' is required\n")
    q(status = 1)
}


# load samples from tab file
samples_df <- read.table(opt$countsFiles, sep = "\t", header = TRUE)
colnames(samples_df) <- c("id", "path")
rownames(samples_df) <- NULL
# Prepare char vector with files and sample names
files <- file.path(samples_df[, "path"])
names(files) <- samples_df[, "id"]



library(tximport)

### if the input is a gff/gtf file first need to create the tx2gene table
if (!is.null(opt$gff_file)) {
    suppressPackageStartupMessages({
        library("GenomicFeatures")
    })
    txdb <- makeTxDbFromGFF(opt$gff_file)
    k <- keys(txdb, keytype = "TXNAME")
    tx2gene <- select(txdb, keys = k, columns = "GENEID", keytype = "TXNAME")
    # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name)
    tx2gene$TXNAME <- sub("^transcript:", "", tx2gene$TXNAME) # nolint
} else {
    tx2gene <- read.table(opt$tx2gene, header = FALSE)
}



##
if (is.null(opt$geneIdCol)) { ## there is a tx2gene table
    if (opt$format == "none") { # predefined format
        txi_out <- tximport(files, type = "none", txIdCol = opt$txIdCol, abundanceCol = opt$abundanceCol, countsCol = opt$countsCol, lengthCol = opt$lengthCol, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
    } else {
        txi_out <- tximport(files, type = opt$format, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
    }
} else { # the gene_ID is a column in the counts table
    if (opt$format == "none") { # predefined format
        txi_out <- tximport(files, type = "none", geneIdCol = opt$geneIdCol, txIdCol = opt$txIdCol, abundanceCol = opt$abundanceCol, countsCol = opt$countsCol, lengthCol = opt$lengthCol, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
    } else {
        txi_out <- tximport(files, type = opt$format, geneIdCol = opt$geneIdCol, countsFromAbundance = opt$countsFromAbundance)
    }
}
# write count as table
write.table(txi_out$counts, file = opt$out_file, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = "\t")