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<tool id="phyloseq_nmds" name="Phyloseq Ordination Plot" version="1.22.3.2" hidden="false">
    <description>Ordination Plotting</description>
    <requirements>
        <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="9.18">ghostscript</requirement>
    </requirements>
    <version_command><![CDATA[
        echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${__tool_directory__}/phyloseq_nmds.R'
        #if str($file_source.file_source_selector) == "set_biom":
            --biom='$file_source.input'
            --subset='$file_source.subsetColumn'
        #else:
            --otu_table='$OTU_TABLE'
            --tax_table='$TAX_TABLE'
            --meta_table='$META_TABLE'
            --category='$file_source.category'
        #end if
        --method='$ord_method'
        --distance='$distance'
        --kingdom='$kingdom_field'
        --cutoff='$cutoff'
        --keep='$keep'
        --filter='$nsample'
        --plottype='$plot_type'
        --outdir="$htmlfile.files_path"
        --htmlfile='$htmlfile'
        ]]>
    </command>

    <inputs>
        <conditional name="file_source">
            <param name="file_source_selector" type="select" label="Choose an input file type">
                <option value="set_biom" selected="True">BIOM File</option>
                <option value="set_table">TABULAR File</option>
            </param>
            <when value="set_biom">
                <param format="biom1" name="input" type="data" label="Input File"/>
                <param name="subsetColumn" type="select" label="Select variable for ordination">
                    <options>
                        <filter type="data_meta" ref="input" key="table_column_metadata_headers" />
                    </options>
                </param>
            </when>
            <when value="set_table">
                <param format="tabular" name="OTU_TABLE" type="data" label="OTU table"/>
                <param format="tabular" name="TAX_TABLE" type="data" label="Taxonomy table"/>
                <param format="tabular" name="META_TABLE" type="data" label="Metadata table"/>
                <param name="category" type="data_column" data_ref="META_TABLE" use_header_names="True" label="Select variable for ordination"/>
            </when>
        </conditional>
        <param name="ord_method" type="select" display="radio" label="Select Ordination method">
            <option value="NMDS" selected="true">NMDS(Non-metric Multidimensional Scalling)</option>
            <option value="DCA">DCA (Detrended Correspondence Analysis)</option>
            <option value="CCA">CCA (Constrained Correspondence Analysis)</option>
            <option value="RDA">RDA (Redundancy Analysis)</option>
            <option value="DPCoA">DPCoA (Double Principle Coordinate Analysis)</option>
            <option value="MDS">MDS (Multidimensional Scaling)</option>
            <option value="PCoA">PCoA (Principal Coordinate Analysis)</option>
        </param>
        <param name="distance" type="select" display="radio" label="Select Distance method">
            <option value="bray" selected="true">bray (Bray-Curtis distance)</option>
            <option value="gower">gower (Gower's distance)</option>
            <option value="jsd">jds (Jensen-Shannon Divergence)</option>
            <option value="unifrac">unifrac (unweighted UniFrac distance)</option>
            <option value="wunifrac">wunifrac (weighted-UniFrac distance)</option>
        </param>
        <param name="kingdom_field" type="select" display="radio" label="Select a taxonomic rank for the analysis">
            <option value="Kingdom">Kingdom</option>
            <option value="Phylum" selected="true">Phylum</option>
            <option value="Class">Class</option>
            <option value="Order">Order</option>
            <option value="Family">Family</option>
            <option value="Genus">Genus</option>
            <option value="Species">Species</option>
        </param>
        <param name="plot_type" type="select" label="Type of Plot" help="Ordination plot type (Plot OTUs, Plot SAMPLE, Biplot graphic, Split plot graphic)">
            <option value="1">OTU</option>
            <option value="2">SAMPLE</option>
        </param>
        <param name="nsample" size="10" type="float" value="0.5" label="Specify the number of samples to discard" help="i.e. remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples (where 1.0 = 100%)"/>
        <param name="cutoff" size="10" type="integer" value="5" label="specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/>
        <param name="keep" size="10" type="integer" value="5" label="Number of the most abundant taxonomic rank units to keep" help="e.g. Phyla, Class and etc"/>
    </inputs>

    <outputs>
        <data format="html" name="htmlfile" label="${tool.name} - ${ord_method.value_label}_${distance.value_label}.html"/>
    </outputs>

    <tests>
        <test>  <!-- Test #1: Test BIOM format input -->
                <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +biom=test-data/GP.biom +subset=6 +method=NMDS
                +distance=bray +kingdom=Phylum +cutoff=5 +keep=5 +outdir=outputdir +htmlfile=biom_out.html -->
            <conditional name="file_source">
                <param name="file_source_selector" value="set_biom"/>
                <param name="input" value="GP.biom" ftype="biom1" />
                <param name="subsetColumn" value="Primer" />
            </conditional>
            <output name="htmlfile" ftype="html" file="biom_out.html" />
        </test>
        <test>  <!-- Test #2: Test TABULAR format inputs -->
                <!-- Equivalent command (replace + with double dash): Rscript phyloseq_nmds.R +otu_table=test-data/GP_OTU_TABLE.txt
                +tax_table=test-data/GP_TAX_TABLE.txt +meta_table=test-data/GP_SAMPLE_TABLE.txt
                +method="bray" +kingdom=Phylum +cutoff=5 + keep=5 +category=6 +outdir=outputdir +htmlfile=test.html -->
            <conditional name="file_source">
                <param name="file_source_selector" value="set_table" />
                <param name="OTU_TABLE" value="GP_OTU_TABLE.txt" />
                <param name="TAX_TABLE" value="GP_TAX_TABLE.txt" />
                <param name="META_TABLE" value="GP_SAMPLE_TABLE.txt" />
                <param name="category" value="6" />
            </conditional>
            <output name="htmlfile" ftype="html" file="test.html" />
        </test>
    </tests>

    <help>
**What it does**
Creates NMDS plot using R package called phyloseq_.

.. _phyloseq: https://joey711.github.io/phyloseq/plot_ordination-examples.html

-----

**Input**

- **Choose an input file type** - BIOM File or TABULAR file
- **Select variable for ordination** - This column is used to extract unique value from the column of interest for ordination plot
- **OTU TABLE** - this is a OTU matrix
- **Taxonomy TABLE** - this is a TAX matrix
- **Metadata TABLE** - this is a metadata file of the experiment design
- **Select Ordination method** - select ordination method
- **Select Distance method** - select distance method for ordination plot
- **Select a taxonomic rank for the analysis** - select a taxonomy for NMDS plot
- **Specify the number of samples to discard** - Y% of samples to discard (where 1.0 = 100%)
- **specify value of X** - Remove OTUs that do not appear more than X times (e.g., 5 times)
- **Number of the most abundant taxonomic rank units** - taxonomic rank units (e.g. Phyla, Class etc) to keep

-----

=========
Resources
=========

**Wrapper Authors**

QFAB Bioinformatics ([e-mail])
Melbourne Bioinformatics
    </help>
    <citations>
        <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
    </citations>
</tool>