view phyloseq_plot_richness.R @ 0:46a99bd1f10e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
author iuc
date Thu, 03 Mar 2022 13:28:04 +0000
parents
children b85ba18a8f36
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#!/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()