<tool id="mashtree_gt" name="mashtree" version="1.4.6+galaxy0" python_template_version="3.5" profile="16.01">
    <description>Create a tree using Mash distances.</description>
    <requirements>
        <requirement type="package" version="1.4.6">mashtree</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #for $file in $input
            ln -s ${file} ./${file.element_identifier}.fasta &&
        #end for
        mashtree --mindepth ${mindepth} 
                 --genomesize ${genomesize} 
                 --kmerlength ${kmerlength} 
                 --sketch-size ${sketchsize} 
                 --numcpus \${GALAXY_SLOTS:-4} 
                 *.fasta
                 --outmatrix ${matrix}
                 --seed 223
                 > ${mashtree}
    ]]></command>
    <inputs>
        <param label="Genome assembliy collection in FASTA format" name="input" type="data_collection" format="fasta" collection_type="list" />
        <param label="Minimum depth. Use 0 for smart depth" type="integer" name="mindepth" value="0" />
        <param label="Estimated genome size in bp" type="integer" name="genomesize" value="5000000" />
        <param label="Kmer length" type="integer" name="kmerlength" value="21" />
        <param label="Sketch size" type="integer" name="sketchsize" value="10000" />
    </inputs>
    <outputs>
        <data name="mashtree" format="newick" label="${tool.name} on ${on_string} tree" />
        <data name="matrix" format="tabular" label="${tool.name} on ${on_string} distance matrix" hidden="true" />
    </outputs>
    <tests>
        <test>
            <param name="input">
                <collection type="list">
                    <element ftype="fasta" name="SRR13160357" value="SRR13160357.fasta" />
                    <element ftype="fasta" name="SRR13160358" value="SRR13160358.fasta" />
                    <element ftype="fasta" name="SRR13160359" value="SRR13160359.fasta" />
                    <element ftype="fasta" name="SRR13160360" value="SRR13160360.fasta" />
                    <element ftype="fasta" name="SRR13167188" value="SRR13167188.fasta" />
                </collection>
            </param>
            <param name="mindepth" value="0" />
            <param name="genomesize" value="2500000" />
            <param name="kmerlength" value="23" />
            <param name="sketchsize" value="10000" />
            <output name="mashtree" file="tree.dnd" />
            <output name="matrix" file="matrix.tsv" />
        </test>
    </tests>
    <help><![CDATA[
        Create a tree using Mash distances. The tree is created using the Mash distance matrix. The tree is created using the neighbor-joining algorithm. The tree is written in Newick format.
    ]]></help>
    <citations>
        <citation type="bibtex">Katz, L. S., Griswold, T., Morrison, S., Caravas, J., Zhang, S., den Bakker, H.C., Deng, X., and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762</citation>
        <citation type="doi">https://doi.org/10.21105/joss.01762</citation>
    </citations>
</tool>