Mercurial > repos > iuc > phyloseq_plot_richness

annotate phyloseq_from_biom.R @ 2:fb7c4bbe8994 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 07:55:57 +0000
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fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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1 #!/usr/bin/env Rscript
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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3 suppressPackageStartupMessages(library("optparse"))
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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4 suppressPackageStartupMessages(library("phyloseq"))
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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5 suppressPackageStartupMessages(library("tidyverse"))
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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7 option_list <- list(
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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8 make_option(c("--BIOMfilename"), action = "store", dest = "biom", help = "Input BIOM file"),
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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9 make_option(c("--treefilename"), action = "store", dest = "tree", default = NULL, help = "Input Tree newick/nexus file"),
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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10 make_option(c("--parseFunction"), action = "store", dest = "parsefoo", default = "parse_taxonomy_default", help = "Parse function parse_taxonomy_default/read_tree_greengenes"),
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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11 make_option(c("--refseqfilename"), action = "store", dest = "sequences", default = NULL, help = "Input Sequence fasta file"),
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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12 make_option(c("--output"), action = "store", dest = "output", help = "RDS output")
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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13 )
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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15 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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16 args <- parse_args(parser, positional_arguments = TRUE)
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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17 opt <- args$options
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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19 parsefoo <- get(opt$parsefoo)
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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20 phyloseq_obj <- import_biom(
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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21 BIOMfilename = opt$biom,
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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22 treefilename = opt$tree,
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
iuc
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23 refseqfilename = opt$sequences,
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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24 parseFunction = parsefoo
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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25 )
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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27 print(phyloseq_obj)
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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29 # save R object to file
fb7c4bbe8994 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 5ec9f9e81bb9a42dec5c331dd23215ca0b027b2b
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30 saveRDS(phyloseq_obj, file = opt$output, compress = TRUE)