add phyloseq bar chart

tools/phyloseq/phyloseq_plot_bar.R

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+#!/usr/bin/env Rscript
+
+# Load libraries
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+suppressPackageStartupMessages(library("ggplot2"))
+
+option_list <- list(
+  make_option(c("--input"), action = "store", dest = "input", help = "Input file containing a phyloseq object"),
+  make_option(c("--x"), action = "store", dest = "x", help = "Variable for x-axis (e.g., 'Sample', 'Phylum')"),
+  make_option(c("--fill"), action = "store", dest = "fill", help = "Variable for fill color (e.g., 'Genus', 'Order')"),
+  make_option(c("--facet"), action = "store", dest = "facet", default = NULL, help = "Facet by variable (optional)"),
+  make_option(c("--output"), action = "store", dest = "output", help = "Output file (PDF)")
+)
+
+# Parse arguments
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser)
+opt <- args$options
+
+# Load phyloseq object
+physeq <- readRDS(opt$input)
+
+# Generate bar plot
+p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
+
+if (!is.null(opt$facet)) {
+  p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
+}
+
+# Save to output file
+ggsave(opt$output, plot = p, width = 10, height = 8)

tools/phyloseq/phyloseq_plot_bar.xml

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+<tool id="phyloseq_plot_bar" name="Phyloseq: Bar Chart" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+  <description>Generate bar charts from a phyloseq object</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="bio_tools"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+Rscript '${__tool_directory__}/phyloseq_plot_bar.R'
+--input '$input'
+--x '$x'
+--fill '$fill'
+--facet '${facet}'
+--output '$output'
+  ]]></command>
+  <inputs>
+    <expand macro="phyloseq_input"/>
+    <param name="x" type="text" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum)" />
+    <param name="fill" type="text" label="Fill variable" help="Variable to color the bars (e.g., Genus, Order)" />
+    <param name="facet" type="text" optional="true" label="Facet by variable" help="Optional: Variable to facet the chart by (e.g., SampleType)" />
+  </inputs>
+  <outputs>
+    <data name="output" format="pdf" label="Bar Chart (PDF)" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+      <param name="x" value="Sample"/>
+      <param name="fill" value="Genus"/>
+      <param name="facet" value="SampleType"/>
+      <output name="output" ftype="pdf">
+        <assert_contents>
+          <has_text text="%PDF"/>
+          <has_text text="%%EOF"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help>
+    **Description**
+
+    This tool generates bar charts from a phyloseq object using the `plot_bar` function.
+
+    **Inputs**
+
+    - **Input**: A phyloseq object in RDS format.
+    - **X-axis variable**: The variable to use for the x-axis (e.g., Sample, Phylum).
+    - **Fill variable**: The variable to use for the bar fill colors (e.g., Genus, Order).
+    - **Facet by variable**: (Optional) A variable to facet the bar chart (e.g., SampleType).
+
+    **Outputs**
+
+    - A PDF file containing the bar chart.
+
+    **Usage Notes**
+
+    Ensure that the input file is a valid phyloseq object in RDS format.
+  </help>
+  <expand macro="citations"/>
+</tool>