| Previous changeset 0:206a71a69161 (2019-12-04) Next changeset 2:1906cb429215 (2021-11-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418" |
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modified:
tximport.R tximport.xml |
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| diff -r 206a71a69161 -r 2c338211927c tximport.R --- a/tximport.R Wed Dec 04 05:57:26 2019 -0500 +++ b/tximport.R Thu Sep 23 00:18:22 2021 +0000 |
| [ |
| @@ -1,5 +1,7 @@ # setup R error handling to go to stderr -options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +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") @@ -19,46 +21,46 @@ "gff_file", "H", 0, "character", "tx2gene", "f", 0, "character", "geneIdCol", "l", 0, "character", - "txIdCol" , "p", 1, "character", + "txIdCol", "p", 1, "character", "abundanceCol", "i", 0, "character", "countsCol", "y", 1, "character", "lengthCol", "x", 1, "character"), - byrow=TRUE, ncol=4) + 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$help)) { - cat(getopt(spec, usage=TRUE)) - q(status=1) + cat(getopt(spec, usage = TRUE)) + q(status = 1) } if (is.null(opt$gff_file) & is.null(opt$tx2gene)) { cat("A GFF/GTF file or a tx2gene table is required\n") - q(status=1) + q(status = 1) } -if (opt$format == 'none'){ #custom format +if (opt$format == "none") { #custom format if (is.null(opt$txIdCol) | is.null(opt$abundanceCol) | is.null(opt$countsCol) | is.null(opt$lengthCol)) { cat("If you select a custom format for the input files you need to specify the column names\n") - q(status=1) + q(status = 1) } } if (is.null(opt$countsFiles)) { cat("'countsFiles' is required\n") - q(status=1) + q(status = 1) } # load samples from tab file -samples_df <- read.table(opt$countsFiles, sep="\t", header=TRUE) -colnames(samples_df) <- c("id","path") +samples_df <- read.table(opt$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"] +# Prepare char vector with files and sample names +files <- file.path(samples_df[, "path"]) +names(files) <- samples_df[, "id"] @@ -71,30 +73,30 @@ }) txdb <- makeTxDbFromGFF(opt$gff_file) k <- keys(txdb, keytype = "TXNAME") - tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME") + tx2gene <- select(txdb, keys = k, columns = "GENEID", keytype = "TXNAME") # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name) - tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME) + tx2gene$TXNAME <- sub("^transcript:", "", tx2gene$TXNAME) # nolint } else { - tx2gene <- read.table(opt$tx2gene,header=FALSE) + 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) + 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) + 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$countsFromAbundance) + if (opt$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$countsFromAbundance) + txi_out <- tximport(files, type = opt$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") +write.table(txi_out$counts, file = opt$out_file, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = "\t") |
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| diff -r 206a71a69161 -r 2c338211927c tximport.xml --- a/tximport.xml Wed Dec 04 05:57:26 2019 -0500 +++ b/tximport.xml Thu Sep 23 00:18:22 2021 +0000 |
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| @@ -1,9 +1,15 @@ -<tool id="tximport" name="tximport" version="0.1"> +<tool id="tximport" name="tximport" version="@TOOL_VERSION@" profile="20.09"> + <macros> + <token name="@TOOL_VERSION@">1.20.0</token> + </macros> <description>Summarize transcript-level estimates for gene-level analysis</description> + <xrefs> + <xref type="bio.tools">tximport</xref> + </xrefs> <requirements> - <requirement type="package">bioconductor-tximport</requirement> - <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement> - <requirement type="package" version="1.20.2">r-getopt</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-tximport</requirement> + <requirement type="package" version="1.44.0">bioconductor-genomicfeatures</requirement> + <requirement type="package" version="1.20.3">r-getopt</requirement> </requirements> <stdio> @@ -123,9 +129,9 @@ </conditional> <param name="counts_from_abundance" type="select" label="Summarization using the abundance (TPM) values?"> <option value="no">No</option> - <option value="scaled_TPM">Scaled up to library size</option> - <option value="length_scaled_TPM">Scaled using the avg. transcript legth over samples and then the library size</option> - <option value="dtu_scaled_TPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option> + <option value="scaledTPM">Scaled up to library size</option> + <option value="lengthScaledTPM">Scaled using the avg. transcript legth over samples and then the library size</option> + <option value="dtuScaledTPM">Scaled using the median transcript length among isoforms of a gene, and then the library size</option> </param> </inputs> <outputs> |