<tool id="get_organelle" name="Assemble organelle genome from genomic skimming data" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="1.7.6.1">getorganelle</requirement>
        <requirement type="package" version="0.0.1">getorganelledb</requirement>
        <requirement type="set_environment">GETORGANELLEDB</requirement>

    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        get_organelle_from_reads.py -1 '$fastq1' -2 '$fastq2' -t 10 -o assembly_dir --config-dir \${GETORGANELLEDB} -F ${ref_db} &&
        cat assembly_dir/*.fasta > ${assembly_contigs} &&
        zip -r assembly.zip assembly_dir &&
        mv assembly.zip ${assembly_zip}


    ]]></command>
    <inputs>
        <param type="data" name="fastq1" format="fastq" help="FASTQ forward reads"/>
        <param type="data" name="fastq2" format="fastq" help="FASTQ reverse reads" />
        <param type="select" label="Assembly type" name="ref_db" >
            <option value="embplant_pt" selected="true" > Embryophyta plant plastome </option>
            <option value="embplant_mt">Embryophyta plant mitogenome </option>
            <option value="embplant_nr">Embryophyta plant ribosomal RNA </option>
            <option value="other_pt">Non-embryophyta plant plastome </option>
            <option value="animal_mt">Animal mitogenome </option>
            <option value="fungus_mt">Fungus mitogenome </option>
            <option value="fungus_nr">Fungus ribosomal RNA </option>
        </param>
    </inputs>
    <outputs>
        <data name="assembly_contigs" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (contigs)" />
        <data name="assembly_zip" format="fasta" label="Assembly from ${on_string} using ${ref_db} database (full results as archive)" />
    </outputs>
    <help><![CDATA[
        This toolkit assemblies organelle genome from genomic skimming data.

        Citation: Jian-Jun Jin*, Wen-Bin Yu*, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi, De-Zhu Li. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology 21, 241 (2020). https://doi.org/10.1186/s13059-020-02154-5

        Source code - https://github.com/Kinggerm/GetOrganelle

        Organelle Database -  https://github.com/Kinggerm/GetOrganelleDB

    ]]></help>
</tool>