--- a/tximport.R	Tue Nov 09 22:44:59 2021 +0000
+++ b/tximport.R	Sat Sep 28 16:33:19 2024 +0000
@@ -1,6 +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)
+    cat(geterrmessage(), file = stderr())
+    q("no", 1, F)
 })
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
@@ -12,45 +13,48 @@
 
 # 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)
+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)
+    cat(getopt(spec, usage = TRUE))
+    q(status = 1)
 }
 
-if (opt$format == "none") {  #custom format
+if (is.null(opt$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)
+    cat("'countsFiles' is required\n")
+    q(status = 1)
 }
 
 
@@ -75,28 +79,26 @@
     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
-
+    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
+    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$format == "none") {  #predefined format
+} else { # the gene_ID is a column in the counts table
+    if (opt$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")

--- a/tximport.xml	Tue Nov 09 22:44:59 2021 +0000
+++ b/tximport.xml	Sat Sep 28 16:33:19 2024 +0000
@@ -1,15 +1,16 @@
 <tool id="tximport" name="tximport" version="@TOOL_VERSION@" profile="20.09">
     <macros>
-        <token name="@TOOL_VERSION@">1.22.0</token>
+        <token name="@TOOL_VERSION@">1.30.0</token>
     </macros>
     <description>Summarize transcript-level estimates for gene-level analysis</description>
     <xrefs>
         <xref type="bio.tools">tximport</xref>
+        <xref type="bioconductor">tximport</xref>
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-tximport</requirement>
-        <requirement type="package" version="1.46.1">bioconductor-genomicfeatures</requirement>
-        <requirement type="package" version="1.20.3">r-getopt</requirement>
+        <requirement type="package" version="1.54.1">bioconductor-genomicfeatures</requirement>
+        <requirement type="package" version="1.20.4">r-getopt</requirement>
     </requirements>
 
     <stdio>
@@ -209,6 +210,6 @@
 Take into account that DEseq2 package in Galaxy requires one table per sample.
     ]]></help>
     <citations>
-        <citation type="doi">doi:10.18129/B9.bioc.tximport</citation>
+        <citation type="doi">10.18129/B9.bioc.tximport</citation>
     </citations>
 </tool>