Mercurial > repos > iuc > phyloseq_plot_richness
changeset 1:1ff178d1757e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2
| author | iuc |
|---|---|
| date | Fri, 09 Feb 2024 21:42:16 +0000 |
| parents | 92b82deaaed1 |
| children | fb7c4bbe8994 |
| files | macros.xml phyloseq_from_dada2.R phyloseq_plot_ordination.R phyloseq_plot_richness.R phyloseq_plot_richness.xml |
| diffstat | 5 files changed, 32 insertions(+), 36 deletions(-) [+] |
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--- a/macros.xml Thu Mar 03 13:28:55 2022 +0000 +++ b/macros.xml Fri Feb 09 21:42:16 2024 +0000 @@ -2,6 +2,11 @@ <token name="@TOOL_VERSION@">1.38.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">21.01</token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">phyloseq</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-phyloseq</requirement>
--- a/phyloseq_from_dada2.R Thu Mar 03 13:28:55 2022 +0000 +++ b/phyloseq_from_dada2.R Fri Feb 09 21:42:16 2024 +0000 @@ -10,30 +10,25 @@ make_option(c("--output"), action = "store", dest = "output", help = "RDS output") ) -parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); -args <- parse_args(parser, positional_arguments = TRUE); -opt <- args$options; - +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args <- parse_args(parser, positional_arguments = TRUE) +opt <- args$options # The input sequence_table is an integer matrix # stored as tabular (rows = samples, columns = ASVs). -seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, sep = "\t")); - +seq_table_numeric_matrix <- data.matrix(read.table(opt$sequence_table, sep = "\t")) # The input taxonomy_table is a table containing # the assigned taxonomies exceeding the minBoot # level of bootstrapping confidence. Rows correspond # to sequences, columns to taxonomic levels. NA # indicates that the sequence was not consistently # classified at that level at the minBoot threshold. -tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = FALSE, sep = "\t")); - +tax_table_matrix <- as.matrix(read.table(opt$taxonomy_table, header = FALSE, sep = "\t")) # Construct a tax_table object. The rownames of # tax_tab must match the OTU names (taxa_names) # of the otu_table defined below. -tax_tab <- tax_table(tax_table_matrix); - +tax_tab <- tax_table(tax_table_matrix) # Construct an otu_table object. -otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE); - +otu_tab <- otu_table(seq_table_numeric_matrix, taxa_are_rows = TRUE) # Construct a phyloseq object. -phyloseq_obj <- phyloseq(otu_tab, tax_tab); -saveRDS(phyloseq_obj, file = opt$output, compress = TRUE); +phyloseq_obj <- phyloseq(otu_tab, tax_tab) +saveRDS(phyloseq_obj, file = opt$output, compress = TRUE)
--- a/phyloseq_plot_ordination.R Thu Mar 03 13:28:55 2022 +0000 +++ b/phyloseq_plot_ordination.R Fri Feb 09 21:42:16 2024 +0000 @@ -11,20 +11,17 @@ make_option(c("--output"), action = "store", dest = "output", help = "Output") ) -parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); -args <- parse_args(parser, positional_arguments = TRUE); -opt <- args$options; - +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args <- parse_args(parser, positional_arguments = TRUE) +opt <- args$options # Construct a phyloseq object. -phyloseq_obj <- readRDS(opt$input); - +phyloseq_obj <- readRDS(opt$input) # Transform data to proportions as appropriate for # Bray-Curtis distances. -proportions_obj <- transform_sample_counts(phyloseq_obj, function(otu) otu / sum(otu)); -ordination_obj <- ordinate(proportions_obj, method = opt$method, distance = opt$distance); - +proportions_obj <- transform_sample_counts(phyloseq_obj, function(otu) otu / sum(otu)) +ordination_obj <- ordinate(proportions_obj, method = opt$method, distance = opt$distance) # Start PDF device driver and generate the plot. -dev.new(); -pdf(file = opt$output); -plot_ordination(proportions_obj, ordination_obj, type = opt$type); -dev.off(); +dev.new() +pdf(file = opt$output) +plot_ordination(proportions_obj, ordination_obj, type = opt$type) +dev.off()
--- a/phyloseq_plot_richness.R Thu Mar 03 13:28:55 2022 +0000 +++ b/phyloseq_plot_richness.R Fri Feb 09 21:42:16 2024 +0000 @@ -8,14 +8,12 @@ make_option(c("--output"), action = "store", dest = "output", help = "Output PDF") ) -parser <- OptionParser(usage = "%prog [options] file", option_list = option_list); -args <- parse_args(parser, positional_arguments = TRUE); -opt <- args$options; - -phyloseq_obj <- readRDS(opt$input); - +parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) +args <- parse_args(parser, positional_arguments = TRUE) +opt <- args$options +phyloseq_obj <- readRDS(opt$input) # Start PDF device driver and generate the plot. -dev.new(); -pdf(file = opt$output); -plot_richness(phyloseq_obj, x = "samples", color = "samples"); +dev.new() +pdf(file = opt$output) +plot_richness(phyloseq_obj, x = "samples", color = "samples") dev.off()
--- a/phyloseq_plot_richness.xml Thu Mar 03 13:28:55 2022 +0000 +++ b/phyloseq_plot_richness.xml Fri Feb 09 21:42:16 2024 +0000 @@ -3,6 +3,7 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ Rscript '${__tool_directory__}/phyloseq_plot_richness.R'