# HG changeset patch
# User iuc
# Date 1707514929 0
# Node ID 92e77800ef2cbed4387a71f1dec82ea1b9c4b1cf
# Parent  11d43fa12aab71f18db36a0463a1359c956b0985
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 7df921baa7aa8680421b9440a1cd6eaab1a15ce2

diff -r 11d43fa12aab -r 92e77800ef2c macros.xml
--- a/macros.xml	Thu Mar 03 13:28:30 2022 +0000
+++ b/macros.xml	Fri Feb 09 21:42:09 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>
diff -r 11d43fa12aab -r 92e77800ef2c phyloseq_from_dada2.R
--- a/phyloseq_from_dada2.R	Thu Mar 03 13:28:30 2022 +0000
+++ b/phyloseq_from_dada2.R	Fri Feb 09 21:42:09 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)
diff -r 11d43fa12aab -r 92e77800ef2c phyloseq_plot_ordination.R
--- a/phyloseq_plot_ordination.R	Thu Mar 03 13:28:30 2022 +0000
+++ b/phyloseq_plot_ordination.R	Fri Feb 09 21:42:09 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()
diff -r 11d43fa12aab -r 92e77800ef2c phyloseq_plot_ordination.xml
--- a/phyloseq_plot_ordination.xml	Thu Mar 03 13:28:30 2022 +0000
+++ b/phyloseq_plot_ordination.xml	Fri Feb 09 21:42:09 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_ordination.R' 
diff -r 11d43fa12aab -r 92e77800ef2c phyloseq_plot_richness.R
--- a/phyloseq_plot_richness.R	Thu Mar 03 13:28:30 2022 +0000
+++ b/phyloseq_plot_richness.R	Fri Feb 09 21:42:09 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()