diff get_deseq_dataset.R @ 44:1cb33de18af5 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594

--- a/get_deseq_dataset.R	Tue Jul 18 14:58:28 2023 +0000
+++ b/get_deseq_dataset.R	Tue Dec 09 17:43:58 2025 +0000
@@ -1,80 +1,77 @@
 get_deseq_dataset <- function(sample_table, header, design_formula, tximport, txtype, tx2gene) {
-
-  dir <- ""
+    dir <- ""
 
-  has_header <- !is.null(header)
-  use_txi <- !is.null(tximport)
-  if (use_txi) {
-    if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport")
-    if (tolower(file_ext(tx2gene)) == "gff") {
-      gff_file <- tx2gene
-    } else {
-      gff_file <- NULL
-      tx2gene <- read.table(tx2gene, header = has_header)
+    has_header <- !is.null(header)
+    use_txi <- !is.null(tximport)
+    if (use_txi) {
+        if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport")
+        if (tolower(file_ext(tx2gene)) == "gff") {
+            gff_file <- tx2gene
+        } else {
+            gff_file <- NULL
+            tx2gene <- read.table(tx2gene, header = has_header)
+        }
     }
-  }
 
-  if (!use_txi && has_header) {
-      countfiles <- lapply(as.character(sample_table$filename), read.delim, row.names = 1)
-      tbl <- do.call("cbind", countfiles)
-      colnames(tbl) <- rownames(sample_table) # take sample ids from header
+    if (!use_txi && has_header) {
+        countfiles <- lapply(as.character(sample_table$filename), read.delim, row.names = 1)
+        tbl <- do.call("cbind", countfiles)
+        colnames(tbl) <- rownames(sample_table) # take sample ids from header
 
-      # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
-      old_special_names <- c(
-        "no_feature",
-        "ambiguous",
-        "too_low_aQual",
-        "not_aligned",
-        "alignment_not_unique"
-      )
-      special_rows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% old_special_names
-      tbl <- tbl[!special_rows, , drop = FALSE]
-
-      dds <- DESeqDataSetFromMatrix(
-        countData = tbl,
-        colData = subset(sample_table, select = -filename),
-        design = design_formula
-      )
-  } else if (!use_txi && !has_header) {
+        # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
+        old_special_names <- c(
+            "no_feature",
+            "ambiguous",
+            "too_low_aQual",
+            "not_aligned",
+            "alignment_not_unique"
+        )
+        special_rows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% old_special_names
+        tbl <- tbl[!special_rows, , drop = FALSE]
 
-    # construct the object from HTSeq files
-    dds <- DESeqDataSetFromHTSeqCount(
-      sampleTable = sample_table,
-      directory = dir,
-      design = design_formula
-    )
-    colnames(dds) <- row.names(sample_table)
-
-  } else {
-      # construct the object using tximport
-      library("tximport")
-      txi_files <- as.character(sample_table$filename)
-      labs <- row.names(sample_table)
-      names(txi_files) <- labs
-      if (!is.null(gff_file)) {
-        # first need to make the tx2gene table
-        # this takes ~2-3 minutes using Bioconductor functions
-        suppressPackageStartupMessages({
-          library("GenomicFeatures")
-        })
-        txdb <- makeTxDbFromGFF(gff_file)
-        k <- keys(txdb, keytype = "TXNAME")
-        tx2gene <- select(txdb, keys = k, columns = "GENEID", keytype = "TXNAME")
-        # Remove 'transcript:' from transcript IDs (when gff_file is a GFF3 from Ensembl and the transcript does not have a Name)
-        tx2gene$TXNAME <- sub("^transcript:", "", tx2gene$TXNAME)  # nolint
-      }
-      try(txi <- tximport(txi_files, type = txtype, tx2gene = tx2gene))
-      if (!exists("txi")) {
-        # Remove version from transcript IDs in tx2gene...
-        tx2gene$TXNAME <- sub("\\.[0-9]+$", "", tx2gene$TXNAME)  # nolint
-        # ...and in txi_files
-        txi <- tximport(txi_files, type = txtype, tx2gene = tx2gene, ignoreTxVersion = TRUE)
-      }
-      dds <- DESeqDataSetFromTximport(
-        txi,
-        subset(sample_table, select = -c(filename)),
-        design_formula
-      )
-  }
-  return(dds)
+        dds <- DESeqDataSetFromMatrix(
+            countData = tbl,
+            colData = subset(sample_table, select = -filename),
+            design = design_formula
+        )
+    } else if (!use_txi && !has_header) {
+        # construct the object from HTSeq files
+        dds <- DESeqDataSetFromHTSeqCount(
+            sampleTable = sample_table,
+            directory = dir,
+            design = design_formula
+        )
+        colnames(dds) <- row.names(sample_table)
+    } else {
+        # construct the object using tximport
+        library("tximport")
+        txi_files <- as.character(sample_table$filename)
+        labs <- row.names(sample_table)
+        names(txi_files) <- labs
+        if (!is.null(gff_file)) {
+            # first need to make the tx2gene table
+            # this takes ~2-3 minutes using Bioconductor functions
+            suppressPackageStartupMessages({
+                library("GenomicFeatures")
+            })
+            txdb <- makeTxDbFromGFF(gff_file)
+            k <- keys(txdb, keytype = "TXNAME")
+            tx2gene <- select(txdb, keys = k, columns = "GENEID", keytype = "TXNAME")
+            # Remove 'transcript:' from transcript IDs (when gff_file is a GFF3 from Ensembl and the transcript does not have a Name)
+            tx2gene$TXNAME <- sub("^transcript:", "", tx2gene$TXNAME) # nolint
+        }
+        try(txi <- tximport(txi_files, type = txtype, tx2gene = tx2gene))
+        if (!exists("txi")) {
+            # Remove version from transcript IDs in tx2gene...
+            tx2gene$TXNAME <- sub("\\.[0-9]+$", "", tx2gene$TXNAME) # nolint
+            # ...and in txi_files
+            txi <- tximport(txi_files, type = txtype, tx2gene = tx2gene, ignoreTxVersion = TRUE)
+        }
+        dds <- DESeqDataSetFromTximport(
+            txi,
+            subset(sample_table, select = -c(filename)),
+            design_formula
+        )
+    }
+    return(dds)
 }