diff phyloseq_plot_richness.R @ 1:b85ba18a8f36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2

--- a/phyloseq_plot_richness.R	Thu Mar 03 13:28:04 2022 +0000
+++ b/phyloseq_plot_richness.R	Fri Feb 09 21:42:24 2024 +0000
@@ -8,14 +8,12 @@
     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);
-
+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$output);
-plot_richness(phyloseq_obj, x = "samples", color = "samples");
+dev.new()
+pdf(file = opt$output)
+plot_richness(phyloseq_obj, x = "samples", color = "samples")
 dev.off()