Mercurial > repos > iuc > phyloseq_plot_richness
comparison phyloseq_from_biom.R @ 2:fb7c4bbe8994 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
| author | iuc |
|---|---|
| date | Sat, 16 Mar 2024 07:55:57 +0000 |
| parents | |
| children |
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| 1:1ff178d1757e | 2:fb7c4bbe8994 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 suppressPackageStartupMessages(library("optparse")) | |
| 4 suppressPackageStartupMessages(library("phyloseq")) | |
| 5 suppressPackageStartupMessages(library("tidyverse")) | |
| 6 | |
| 7 option_list <- list( | |
| 8 make_option(c("--BIOMfilename"), action = "store", dest = "biom", help = "Input BIOM file"), | |
| 9 make_option(c("--treefilename"), action = "store", dest = "tree", default = NULL, help = "Input Tree newick/nexus file"), | |
| 10 make_option(c("--parseFunction"), action = "store", dest = "parsefoo", default = "parse_taxonomy_default", help = "Parse function parse_taxonomy_default/read_tree_greengenes"), | |
| 11 make_option(c("--refseqfilename"), action = "store", dest = "sequences", default = NULL, help = "Input Sequence fasta file"), | |
| 12 make_option(c("--output"), action = "store", dest = "output", help = "RDS output") | |
| 13 ) | |
| 14 | |
| 15 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) | |
| 16 args <- parse_args(parser, positional_arguments = TRUE) | |
| 17 opt <- args$options | |
| 18 | |
| 19 parsefoo <- get(opt$parsefoo) | |
| 20 phyloseq_obj <- import_biom( | |
| 21 BIOMfilename = opt$biom, | |
| 22 treefilename = opt$tree, | |
| 23 refseqfilename = opt$sequences, | |
| 24 parseFunction = parsefoo | |
| 25 ) | |
| 26 | |
| 27 print(phyloseq_obj) | |
| 28 | |
| 29 # save R object to file | |
| 30 saveRDS(phyloseq_obj, file = opt$output, compress = TRUE) |