<tool id="phyloseq_plot_ordination" name="Phyloseq: plot ordination" 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 '${__tool_directory__}/phyloseq_plot_ordination.R' 
--input '$input' 
--method '$method'
--distance '$distance'
--type '$type'
--output '$output'
    ]]></command>
    <inputs>
        <expand macro="phyloseq_input"/>
        <param name="method" type="select" label="Ordination method">
            <option value="DCA" selected="true">DCA</option>
            <option value="CCA">CCA</option>
            <option value="RDA">RDA</option>
            <option value="CAP">CAP</option>
            <option value="NMDS">NMDS</option>
            <option value="MDS">MDS</option>
            <option value="PCoA">PCoA</option>
        </param>
        <param name="distance" type="select" label="Distance method" help="Utilized only if a distance matrix is required by the Ordination method selected above">
            <option value="bray" selected="true">bray</option>
            <option value="canberra">canberra</option>
            <option value="euclidean">euclidean</option>
            <option value="gower">gower</option>
            <option value="horn">horn</option>
            <option value="jaccard">jaccard</option>
            <option value="kulczynski">kulczynski</option>
            <option value="manhattan">manhattan</option>
            <option value="maximum">maximum</option>
            <option value="minkowski">minkowski</option>
            <option value="morisita">morisita</option>
            <option value="mountford">mountford</option>
        </param>
        <param name="type" type="select" label="Plot type">
            <option value="biplot" selected="true">biplot</option>
            <option value="samples">samples</option>
            <option value="scree">scree</option>
            <option value="species">species</option>
            <option value="split">split</option>
        </param>
    </inputs>
    <expand macro="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,
and generates an ordination plot of the samples.

**Options**

 **Ordination method**

  * **DCA** - Performs detrended correspondence analysis using decorana.
  * **CCA** - Performs correspondence analysis, or optionally, constrained correspondence analysis (a.k.a. canonical correspondence analysis) via vegan cca.
  * **RDA** - Performs redundancy analysis, or optionally principal components analysis, via vegan rda.
  * **CAP** - [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA, via vegan capscale.
  * **NMDS** - Performs Non-metric MultiDimenstional Scaling of a sample-wise ecological distance matrix onto a user-specified number of axes (k).  
  * **MDS/PCoA** - Performs principal coordinate analysis (also called principle coordinate decomposition, multidimensional scaling (MDS), or classical scaling) of a distance matrix including two correction methods for negative eigenvalues.

 **Distance method** - Utilized only if a distance matrix is required by the Ordination method documented above.

 **Plot type**

  * **biplot** - Produces a combined plot with both taxa and samples.
  * **samples** - Produces a single plot of just the samples of the ordination.
  * **scree** - Produces an ordered bar plot of the normalized eigenvalues associated with each ordination axis.
  * **species** - Produces a single plot of just the species of the ordination.
  * **split** - Produces a plot with both taxa and samples separated in two facet panels respectively.
    </help>
    <expand macro="citations"/>
</tool>