diff phyloseq_from_dada2.R @ 0:c0101c72b8af draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_from_dada2.R	Sat Mar 16 07:56:17 2024 +0000
@@ -0,0 +1,55 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+suppressPackageStartupMessages(library("tidyverse"))
+
+option_list <- list(
+    make_option(c("--sequence_table"), action = "store", dest = "sequence_table", help = "Input sequence table"),
+    make_option(c("--taxonomy_table"), action = "store", dest = "taxonomy_table", help = "Input taxonomy table"),
+    make_option(c("--sample_table"), action = "store", default = NULL, dest = "sample_table", help = "Input sample table"),
+    make_option(c("--output"), action = "store", dest = "output", help = "RDS output")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser, positional_arguments = TRUE)
+opt <- args$options
+# The input sequence_table is an integer matrix
+# stored as tabular (rows = samples, columns = ASVs).
+seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, header = T, sep = "\t", row.names = 1, check.names = FALSE))
+# The input taxonomy_table is a table containing
+# the assigned taxonomies exceeding the minBoot
+# level of bootstrapping confidence. Rows correspond
+# to sequences, columns to taxonomic levels. NA
+# indicates that the sequence was not consistently
+# classified at that level at the minBoot threshold.
+tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = T, sep = "\t", row.names = 1, check.names = FALSE))
+# Construct a tax_table object.  The rownames of
+# tax_tab must match the OTU names (taxa_names)
+# of the otu_table defined below.
+tax_tab <- tax_table(tax_table_matrix)
+
+# Construct an otu_table object.
+otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE)
+
+# Construct a phyloseq object.
+phyloseq_obj <- phyloseq(otu_tab, tax_tab)
+if (!is.null(opt$sample_table)) {
+    sample_tab <- sample_data(
+        read.table(opt$sample_table, header = T, sep = "\t", row.names = 1, check.names = FALSE)
+    )
+    phyloseq_obj <- merge_phyloseq(phyloseq_obj, sample_tab)
+}
+
+# use short names for our ASVs and save the ASV sequences
+# refseq slot of the phyloseq object as described in
+# https://benjjneb.github.io/dada2/tutorial.html
+dna <- Biostrings::DNAStringSet(taxa_names(phyloseq_obj))
+names(dna) <- taxa_names(phyloseq_obj)
+phyloseq_obj <- merge_phyloseq(phyloseq_obj, dna)
+taxa_names(phyloseq_obj) <- paste0("ASV", seq(ntaxa(phyloseq_obj)))
+
+print(phyloseq_obj)
+
+# save R object to file
+saveRDS(phyloseq_obj, file = opt$output, compress = TRUE)