Mercurial > repos > iuc > phyloseq_plot_richness

comparison phyloseq_plot_richness.R @ 1:b6b41cf9c30a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 10dfb1308ff858c6623c7dd9215a3bdf518427f9
author iuc
date Tue, 03 Dec 2024 17:44:32 +0000
parents 7a27e9711e4e
children
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0:7a27e9711e4e 1:b6b41cf9c30a
6 option_list <- list( 6 option_list <- list(
7 make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"), 7 make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"),
8 make_option(c("--output"), action = "store", dest = "output", help = "Output PDF") 8 make_option(c("--output"), action = "store", dest = "output", help = "Output PDF")
9 ) 9 )
10 10
11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); 11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
12 args <- parse_args(parser, positional_arguments = TRUE); 12 args <- parse_args(parser, positional_arguments = TRUE)
13 opt <- args$options; 13 opt <- args$options
14 14 phyloseq_obj <- readRDS(opt$input)
15 phyloseq_obj <- readRDS(opt$input);
16
17 # Start PDF device driver and generate the plot. 15 # Start PDF device driver and generate the plot.
18 dev.new(); 16 dev.new()
19 pdf(file = opt$output); 17 pdf(file = opt$output)
20 plot_richness(phyloseq_obj, x = "samples", color = "samples"); 18 plot_richness(phyloseq_obj, x = "samples", color = "samples")
21 dev.off() 19 dev.off()