Mercurial > repos > iuc > phyloseq_from_biom
view phyloseq_from_biom.R @ 1:1feea247d08a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
author | iuc |
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date | Tue, 03 Dec 2024 17:45:38 +0000 |
parents | c0101c72b8af |
children |
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#!/usr/bin/env Rscript suppressPackageStartupMessages(library("optparse")) suppressPackageStartupMessages(library("phyloseq")) suppressPackageStartupMessages(library("tidyverse")) option_list <- list( make_option(c("--BIOMfilename"), action = "store", dest = "biom", help = "Input BIOM file"), make_option(c("--treefilename"), action = "store", dest = "tree", default = NULL, help = "Input Tree newick/nexus file"), make_option(c("--parseFunction"), action = "store", dest = "parsefoo", default = "parse_taxonomy_default", help = "Parse function parse_taxonomy_default/read_tree_greengenes"), make_option(c("--refseqfilename"), action = "store", dest = "sequences", default = NULL, help = "Input Sequence fasta file"), 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$options parsefoo <- get(opt$parsefoo) phyloseq_obj <- import_biom( BIOMfilename = opt$biom, treefilename = opt$tree, refseqfilename = opt$sequences, parseFunction = parsefoo ) print(phyloseq_obj) # save R object to file saveRDS(phyloseq_obj, file = opt$output, compress = TRUE)