Mercurial > repos > iuc > phyloseq_plot_ordination

annotate add_rank_names_to_phyloseq.R @ 5:e8f58a93ff19 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d905841a8c8eff6a2006492ef52b31f969e8206a
author iuc
date Tue, 07 Jan 2025 17:58:14 +0000
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1 #!/usr/bin/env Rscript
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3 suppressPackageStartupMessages(library("optparse"))
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4 suppressPackageStartupMessages(library("phyloseq"))
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5 suppressPackageStartupMessages(library("tidyverse"))
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7 # Option parsing
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8 option_list <- list(
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9 make_option(c("--input"),
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10 action = "store", dest = "input",
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11 help = "Input file containing a phyloseq object"
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12 ),
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13 make_option(c("--output"),
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14 action = "store", dest = "output",
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15 help = "Output file for the updated phyloseq object"
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16 ),
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17 make_option(c("--ranks"),
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18 action = "store", dest = "ranks",
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19 help = "Comma-separated list of taxonomy ranks (default: Kingdom,Phylum,Class,Order,Family,Genus,Species)"
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20 )
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21 )
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23 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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24 args <- parse_args(parser, positional_arguments = TRUE)
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25 opt <- args$options
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27 cat("Input file: ", opt$input, "\n")
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28 cat("Output file: ", opt$output, "\n")
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29 cat("Ranks provided: ", opt$ranks, "\n")
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31 if (is.null(opt$ranks)) {
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32 opt$ranks <- "Kingdom,Phylum,Class,Order,Family,Genus,Species"
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33 }
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35 # Parse rank names
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36 rank_names <- unlist(strsplit(opt$ranks, ","))
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38 # Load phyloseq object
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39 physeq <- readRDS(opt$input)
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41 # Check if physeq object is loaded successfully
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42 if (is.null(physeq)) {
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43 stop("Error: Failed to load the Phyloseq object. Check the input file.")
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44 }
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46 cat("Phyloseq object successfully loaded.\n")
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47 cat("Class of loaded object: ", class(physeq), "\n")
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49 # Check the current tax_table
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50 cat("Current tax_table:\n")
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51 print(tax_table(physeq))
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54 # Strict check for taxonomy table and provided ranks
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55 if (ncol(tax_table(physeq)) != length(rank_names)) {
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56 stop(
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57 "Error: Number of columns in tax_table does not match the number of provided ranks. ",
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58 "Please ensure the taxonomy table matches the ranks exactly."
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59 )
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60 }
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62 # Set column names to the provided ranks
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63 colnames(tax_table(physeq)) <- rank_names
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65 # Confirm the changes
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66 cat("Updated tax_table:\n")
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67 print(tax_table(physeq))
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69 # Save the updated phyloseq object
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70 saveRDS(physeq, file = opt$output, compress = TRUE)
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71 cat("Updated Phyloseq object saved to: ", opt$output, "\n")