Merge pull request galaxyproject#6575 from MaraBesemer/main

add phyloseq bar chart

tools/phyloseq/phyloseq_plot_bar.R

@@ -0,0 +1,74 @@
+#!/usr/bin/env Rscript
+
+# Load libraries
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+suppressPackageStartupMessages(library("ggplot2"))
+
+# Define options
+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", default = NULL,
+        help = "Variable for fill color (e.g., 'Genus', 'Order') (optional)"
+    ),
+    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, positional_arguments = TRUE)
+opt <- args$options
+
+# Validate required options
+if (is.null(opt$input) || opt$input == "") {
+    stop("Error: Input file is required.")
+}
+if (is.null(opt$x) || opt$x == "") {
+    stop("Error: X-axis variable is required.")
+}
+if (is.null(opt$output) || opt$output == "") {
+    stop("Error: Output file is required.")
+}
+
+# Load phyloseq object
+print(paste("Trying to read:", opt$input))
+physeq <- readRDS(opt$input)
+
+# Check if the 'x' and 'fill' variables are valid
+sample_vars <- colnames(sample_data(physeq))
+if (!opt$x %in% sample_vars) {
+    stop(paste("Error: X-axis variable", opt$x, "does not exist in the sample data."))
+}
+
+# Generate bar plot
+p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
+
+# Only facet if the facet variable is provided and exists in the sample data
+if (!is.null(opt$facet) && opt$facet != "") {
+    if (opt$facet %in% sample_vars) {
+        p <- p + facet_wrap(as.formula(paste("~", opt$facet)))
+    } else {
+        warning(paste("Facet variable", opt$facet, "does not exist in the sample data. Faceting will be skipped."))
+    }
+}
+
+# Save to output file using PDF device
+print(paste("Saving plot to:", opt$output))
+pdf(file = opt$output, width = 10, height = 8)
+print(p)
+dev.off()

tools/phyloseq/phyloseq_plot_bar.xml

@@ -0,0 +1,76 @@
+<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 1: Default parameters -->
+    <test>
+        <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+        <param name="x" value="Property"/>
+        <param name="fill" value="Number"/>
+        <param name="facet" value="Property"/>
+        <output name="output" ftype="pdf">
+            <assert_contents>
+                <has_text text="%PDF"/>
+                <has_text text="%%EOF"/>
+            </assert_contents>
+        </output>
+    </test>
+    <!-- Test 2: Valid parameters without facet -->
+    <test>
+        <param name="input" value="output.phyloseq" ftype="phyloseq"/>
+        <param name="x" value="Property"/>
+        <param name="fill" value="Number"/>
+        <param name="facet" value=""/>
+        <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**: (Optional) 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>
+