Mercurial > repos > iuc > phyloseq_plot_ordination

comparison phyloseq_from_dada2.R @ 0:11d43fa12aab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit d1004c06207be773c278e12745aada276b63172e"
author iuc
date Thu, 03 Mar 2022 13:28:30 +0000
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children 92e77800ef2c
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-1:000000000000 0:11d43fa12aab
1 #!/usr/bin/env Rscript
2
3 suppressPackageStartupMessages(library("optparse"))
4 suppressPackageStartupMessages(library("phyloseq"))
5 suppressPackageStartupMessages(library("tidyverse"))
6
7 option_list <- list(
8 make_option(c("--sequence_table"), action = "store", dest = "sequence_table", help = "Input sequence table"),
9 make_option(c("--taxonomy_table"), action = "store", dest = "taxonomy_table", help = "Input taxonomy table"),
10 make_option(c("--output"), action = "store", dest = "output", help = "RDS output")
11 )
12
13 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list);
14 args <- parse_args(parser, positional_arguments = TRUE);
15 opt <- args$options;
16
17 # The input sequence_table is an integer matrix
18 # stored as tabular (rows = samples, columns = ASVs).
19 seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, sep = "\t"));
20
21 # The input taxonomy_table is a table containing
22 # the assigned taxonomies exceeding the minBoot
23 # level of bootstrapping confidence. Rows correspond
24 # to sequences, columns to taxonomic levels. NA
25 # indicates that the sequence was not consistently
26 # classified at that level at the minBoot threshold.
27 tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = FALSE, sep = "\t"));
28
29 # Construct a tax_table object. The rownames of
30 # tax_tab must match the OTU names (taxa_names)
31 # of the otu_table defined below.
32 tax_tab <- tax_table(tax_table_matrix);
33
34 # Construct an otu_table object.
35 otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE);
36
37 # Construct a phyloseq object.
38 phyloseq_obj <- phyloseq(otu_tab, tax_tab);
39 saveRDS(phyloseq_obj, file = opt$output, compress = TRUE);