diff phyloseq_plot_richness.R @ 0:46a99bd1f10e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_plot_richness.R	Thu Mar 03 13:28:04 2022 +0000
@@ -0,0 +1,21 @@
+#!/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()