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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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$input) | ||
|
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||
| # Check if the 'x' and 'fill' variables are valid | ||
| sample_vars <- colnames(sample_data(physeq)) | ||
| if (!opt$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$fill) | ||
|
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| # Only facet if the facet variable is provided and exists in the sample data | ||
| if (!is.null(opt$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() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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** | ||
|
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| This tool generates bar charts from a phyloseq object using the `plot_bar` function. | ||
|
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| **Inputs** | ||
|
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| - **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). | ||
|
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||
| **Outputs** | ||
|
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| - A PDF file containing the bar chart. | ||
|
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| **Usage Notes** | ||
|
|
||
| Ensure that the input file is a valid phyloseq object in RDS format. | ||
| </help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
|
|
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