<tool id="multilocus_genotype" name="Multilocus genotype" version="1.0.0">
    <description>unique combination of alleles for loci</description>
    <requirements>
        <requirement type="package" version="2.1.1">r-adegenet</requirement>
        <requirement type="package" version="5.1">r-ape</requirement>
        <requirement type="package" version="1.11.6">r-data.table</requirement>
        <requirement type="package" version="1.2.2">r-dbplyr</requirement>
        <requirement type="package" version="0.7.6">r-dplyr</requirement>
        <requirement type="package" version="3.0.0">r-ggplot2</requirement>
        <requirement type="package" version="1.20">r-knitr</requirement>
        <requirement type="package" version="1.6.0">r-optparse</requirement>
        <requirement type="package" version="2.8.1">r-poppr</requirement>
        <requirement type="package" version="1.1.2">r-rcolorbrewer</requirement>
        <requirement type="package" version="1.1.1">r-rpostgres</requirement>
        <requirement type="package" version="0.8.1">r-tidyr</requirement>
        <requirement type="package" version="2.5_3">r-vegan</requirement>
        <requirement type="package" version="1.8.0">r-vcfr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set output_plots_dir = 'output_plots_dir'
mkdir $output_plots_dir &&
Rscript '$__tool_directory__/multilocus_genotype.R'
--database_connection_string '$__app__.config.corals_database_connection'
--input_affy_metadata '$input_affy_metadata'
--input_pop_info '$input_pop_info'
--input_vcf '$input_vcf'
--output_stag_db_report '$output_stag_db_report'
&> multilocus_genotype.log;
if [[ $? -ne 0 ]]; then
    cp multilocus_genotype.log '$output_stag_db_report';
    exit 1;
fi]]></command>
    <inputs>
        <param name="input_vcf" type="data" format="vcf" label="VCF file" />
        <param name="input_affy_metadata" type="data" format="tabular" label="Affymetrix 96 well plate file" />
        <param name="input_pop_info" type="data" format="txt" label="Genotype population information file" />
    </inputs>
    <outputs>
        <data name="output_stag_db_report" format="csv" label="${tool.name} (stag db report) on ${on_string}"/>
        <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
            <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input_vcf" value="baitssnv.recode.vcf" ftype="vcf"/>
            <param name="input_affy_metadata" value="affy_metadata.tabular" ftype="tabular"/>
            <param name="input_pop_info" value="pop_info.txt" ftype="txt"/>
            <output name="output_stag_db_report" file="output_stag_db_report.csv" ftype="csv"/>
            <output_collection name="output_plot_collection" type="list">
                <element name="nj_phylogeny.pdf" file="nj_phylogeny.pdf" ftype="pdf" compare="contains"/>
                <element name="missing_data.pdf" file="missing_data.pdf" ftype="pdf" compare="contains"/>
                <element name="percent_breakdown.pdf" file="percent_breakdown.pdf" ftype="pdf" compare="contains"/>
            </output_collection>
        </test>
    </tests>
    <help>
**What it does**

Renders the unique combination of the alleles for two or more loci for each individual. The multilocus genotypes
are critically important for tracking dispersal and population structure of organisms, especially those that
reproduce clonally (plants, sponges, cnidarians, flatworms, annelids, sea stars, and many more).
-----

**Required options**
    </help>
    <citations>
    </citations>
</tool>