Mercurial > repos > iuc > phyloseq_from_biom
diff phyloseq_plot_richness.R @ 0:c0101c72b8af draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
author | iuc |
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date | Sat, 16 Mar 2024 07:56:17 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_plot_richness.R Sat Mar 16 07:56:17 2024 +0000 @@ -0,0 +1,19 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("phyloseq")) + +option_list <- list( + make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"), + make_option(c("--output"), action = "store", dest = "output", help = "Output PDF") +) + +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args <- parse_args(parser, positional_arguments = TRUE) +opt <- args$options +phyloseq_obj <- readRDS(opt$input) +# Start PDF device driver and generate the plot. +dev.new() +pdf(file = opt$output) +plot_richness(phyloseq_obj, x = "samples", color = "samples") +dev.off()