Mercurial > repos > iuc > phyloseq_from_dada2
annotate 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 |
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date | Thu, 03 Mar 2022 13:28:04 +0000 |
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children | b85ba18a8f36 |
rev | line source |
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0
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
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1 #!/usr/bin/env Rscript |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
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2 |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
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3 suppressPackageStartupMessages(library("optparse")) |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
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4 suppressPackageStartupMessages(library("phyloseq")) |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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5 |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
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6 option_list <- list( |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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7 make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"), |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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8 make_option(c("--output"), action = "store", dest = "output", help = "Output PDF") |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
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9 ) |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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10 |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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11 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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12 args <- parse_args(parser, positional_arguments = TRUE); |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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13 opt <- args$options; |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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14 |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
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15 phyloseq_obj <- readRDS(opt$input); |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
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16 |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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17 # Start PDF device driver and generate the plot. |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
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18 dev.new(); |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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19 pdf(file = opt$output); |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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20 plot_richness(phyloseq_obj, x = "samples", color = "samples"); |
46a99bd1f10e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
iuc
parents:
diff
changeset
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21 dev.off() |