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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
author iuc
date Sat, 28 Sep 2024 16:33:10 +0000
parents 3e2f1aef1aac
children
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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1 # setup R error handling to go to stderr
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2 options(show.error.messages = F, error = function() {
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3 cat(geterrmessage(), file = stderr())
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4 q("no", 1, F)
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5 })
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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10 library("getopt")
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11 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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12 args <- commandArgs(trailingOnly = TRUE)
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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14 # get options, using the spec as defined by the enclosed list.
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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15 # we read the options from the default: commandArgs(TRUE).
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16 spec <- matrix(
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17 c(
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18 "help", "h", 0, "logical",
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19 "out_file", "o", 1, "character",
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20 "countsFiles", "n", 1, "character",
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21 "countsFromAbundance", "r", 1, "character",
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22 "format", "v", 1, "character",
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23 "gff_file", "H", 0, "character",
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24 "tx2gene", "f", 0, "character",
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25 "geneIdCol", "l", 0, "character",
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26 "txIdCol", "p", 1, "character",
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27 "abundanceCol", "i", 0, "character",
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28 "countsCol", "y", 1, "character",
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29 "lengthCol", "x", 1, "character"
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30 ),
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31 byrow = TRUE, ncol = 4
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32 )
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34 opt <- getopt(spec)
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36 # if help was asked for print a friendly message
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37 # and exit with a non-zero error code
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38 if (!is.null(opt$help)) {
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39 cat(getopt(spec, usage = TRUE))
915a9dd57e1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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40 q(status = 1)
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41 }
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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42
3
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43 if (is.null(opt$gff_file) & is.null(opt$tx2gene)) {
915a9dd57e1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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44 cat("A GFF/GTF file or a tx2gene table is required\n")
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45 q(status = 1)
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46 }
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48 if (opt$format == "none") { # custom format
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49 if (is.null(opt$txIdCol) | is.null(opt$abundanceCol) | is.null(opt$countsCol) | is.null(opt$lengthCol)) {
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50 cat("If you select a custom format for the input files you need to specify the column names\n")
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51 q(status = 1)
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52 }
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53 }
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55 if (is.null(opt$countsFiles)) {
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56 cat("'countsFiles' is required\n")
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57 q(status = 1)
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58 }
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61 # load samples from tab file
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62 samples_df <- read.table(opt$countsFiles, sep = "\t", header = TRUE)
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63 colnames(samples_df) <- c("id", "path")
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64 rownames(samples_df) <- NULL
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65 # Prepare char vector with files and sample names
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66 files <- file.path(samples_df[, "path"])
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67 names(files) <- samples_df[, "id"]
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71 library(tximport)
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73 ### if the input is a gff/gtf file first need to create the tx2gene table
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74 if (!is.null(opt$gff_file)) {
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75 suppressPackageStartupMessages({
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76 library("GenomicFeatures")
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77 })
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78 txdb <- makeTxDbFromGFF(opt$gff_file)
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79 k <- keys(txdb, keytype = "TXNAME")
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80 tx2gene <- select(txdb, keys = k, columns = "GENEID", keytype = "TXNAME")
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81 # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name)
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82 tx2gene$TXNAME <- sub("^transcript:", "", tx2gene$TXNAME) # nolint
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83 } else {
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84 tx2gene <- read.table(opt$tx2gene, header = FALSE)
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85 }
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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89 ##
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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90 if (is.null(opt$geneIdCol)) { ## there is a tx2gene table
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915a9dd57e1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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91 if (opt$format == "none") { # predefined format
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92 txi_out <- tximport(files, type = "none", txIdCol = opt$txIdCol, abundanceCol = opt$abundanceCol, countsCol = opt$countsCol, lengthCol = opt$lengthCol, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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93 } else {
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94 txi_out <- tximport(files, type = opt$format, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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95 }
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915a9dd57e1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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96 } else { # the gene_ID is a column in the counts table
915a9dd57e1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 5f8e6e70a9d82331367f7a052a76a04c47c5144e
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97 if (opt$format == "none") { # predefined format
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98 txi_out <- tximport(files, type = "none", geneIdCol = opt$geneIdCol, txIdCol = opt$txIdCol, abundanceCol = opt$abundanceCol, countsCol = opt$countsCol, lengthCol = opt$lengthCol, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
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d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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99 } else {
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100 txi_out <- tximport(files, type = opt$format, geneIdCol = opt$geneIdCol, countsFromAbundance = opt$countsFromAbundance)
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101 }
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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102 }
d53de4a14836 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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103 # write count as table
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104 write.table(txi_out$counts, file = opt$out_file, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = "\t")