<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'
--topX '${topX}'
--keepOthers '${keepOthers}'
--keepNonAssigned '${keepNonAssigned}'
--normalize '${normalize}'
--width '${width}'
--height '${height}'
--device '${device}'
  ]]></command>
  <inputs>
    <expand macro="phyloseq_input"/>
    <param name="x" type="text" optional="true" label="X-axis variable" help="Variable for the x-axis (e.g., Sample, Phylum). If not specified, the Samples are taken." />
    <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="Variable to facet the chart by (e.g., SampleType)." />
    <param name="topX" value="10" type="integer" optional="true" label="Top X" help="Only show the ranks with the top X abundance." />
    <param name="keepOthers" type="boolean" label="Keep 'Others'" help="Keep OTUs which are not in top X as 'Others'." />
    <param name="keepNonAssigned" type="boolean" label="Keep Non Assigned" help="Keep OTUs that are not assigned at this rank and label as 'Not Assigned'." />
    <param name="normalize" type="boolean" label="Normalize" help="Normalize abundances to sum to 100%. Normalization is performed before Top X selection." />
    <param name="width" type="float" value="10" optional="true" label="Plot Width" help="Width of the output plot in inches." />
    <param name="height" type="float" value="8" optional="true" label="Plot Height" help="Height of the output plot in inches." />
    <param name="device" type="select" value="pdf" label="Output Device" help="Device to use for the output file. Options include pdf, png, and others.">
      <option value="pdf">PDF</option>
      <option value="png">PNG</option>
      <option value="jpeg">JPEG</option>
      <option value="tiff">TIFF</option>
    </param>
  </inputs>
  <outputs>
    <data name="output" format="pdf" label="Bar Chart (PDF)" />
  </outputs>
  <tests>
    <!-- Test 1: Basic functionality with x and fill variables -->
    <test>
      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
      <param name="x" value="Property"/>
      <param name="fill" value="Phylum"/>
      <param name="device" value="pdf"/>
      <output name="output" ftype="pdf">
        <assert_contents>
          <has_text text="%PDF"/>
          <has_text text="%%EOF"/>
        </assert_contents>
      </output>
    </test>

    <!-- Test 2: TopX filtering and normalization -->
    <test>
      <param name="input" value="output.phyloseq" ftype="phyloseq"/>
      <param name="x" value="Property"/>
      <param name="fill" value="Genus"/>
      <param name="facet" value="SampleType"/>
      <param name="topX" value="10"/>
      <param name="normalize" value="true"/>
      <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).
    - **Width and Height**: Dimensions of the plot in inches (default: 10x8).
    - **Device**: Output format (e.g., pdf, png, jpeg, tiff).

    **Outputs**

    - A file containing the bar chart in the specified format.

    **Usage Notes**

    Ensure that the input file is a valid phyloseq object in RDS format.
  </help>
  <expand macro="citations"/>
</tool>