Mercurial > repos > iuc > phyloseq_plot_ordination

annotate phyloseq_plot_richness.R @ 2:dfe800a3faaf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
author iuc
date Sat, 16 Mar 2024 07:56:05 +0000
parents 92e77800ef2c
children
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11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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1 #!/usr/bin/env Rscript
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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3 suppressPackageStartupMessages(library("optparse"))
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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4 suppressPackageStartupMessages(library("phyloseq"))
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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6 option_list <- list(
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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7 make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"),
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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8 make_option(c("--output"), action = "store", dest = "output", help = "Output PDF")
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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9 )
11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
iuc
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11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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12 args <- parse_args(parser, positional_arguments = TRUE)
92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
iuc
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13 opt <- args$options
92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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14 phyloseq_obj <- readRDS(opt$input)
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11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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15 # Start PDF device driver and generate the plot.
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92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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16 dev.new()
92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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17 pdf(file = opt$output)
92e77800ef2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
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18 plot_richness(phyloseq_obj, x = "samples", color = "samples")
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11d43fa12aab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
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19 dev.off()