<tool id="phyloseq_plot_richness" name="Phyloseq: plot alpha diverstiy measure" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
  <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
Rscript '${__tool_directory__}/phyloseq_plot_richness.R' 
--input '$input' 
--output '$output'
    ]]></command>
    <inputs>
        <expand macro="phyloseq_input"/>
    </inputs>
    <outputs>
        <data name="output" format="pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="output.phyloseq" ftype="phyloseq"/>
            <output name="output" ftype="pdf">
                <assert_contents>
                    <has_text text="%PDF"/>
                    <has_text text="%%EOF"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**What it does**

Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table,
estimates a number of alpha-diversity metrics, and generates a colored plot that includes the alpha diverstiy measure
of each sample. 
    </help>
    <expand macro="citations"/>
</tool>