<tool id="quast-select" name="Select Best" version="0.1.0" profile="16.10">
    <description>assembly based on a combined QUAST table</description>
    <requirements>
        <requirement type="package">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #for $asm in $coll
        ln -s $asm ./$asm.element_identifier &&
        #end for
        cp ./\$(python $__tool_directory__/quast_select.py $table $criterion) $output
    ]]></command>
    <inputs>
        <param type="data" format="tsv" name="table" label="Combined QUAST output (from table_union)"/>
        <param type="select" label="Select best assembly by..." name="criterion">
            <option value="N50">Longest N50</option>
            <option value="Largest contig">Longest single contig</option>
            <option value="# contigs">Fewest contigs</option>
            <option value="# contigs (>= 1000 bp)">Fewest contigs of length 1kbp or longer</option>
            <option value="Total length">Total assembly length</option>
            <option value="Total length (>= 1000 bp)">Total assembly length of contigs longer than 1kbp</option>
        </param>
        <param type="data_collection" collection_type="list" format="fasta" name="coll" label="Collection of FASTA assemblies" />
    </inputs>
    <outputs>
        <data format="fasta" name="output" label="Best assembly by ${criterion}" />
    </outputs>
    <tests>
        <test>
            <param name="table" value="combined_table.tsv" />
            <param name="coll" >
                <collection type="list">
                    <element name="sample1" value="sample1.fasta" />
                    <element name="sample2" value="sample2.fasta" />
                    <element name="sample3" value="sample3.fasta" />
                    <element name="sample4" value="sample4.fasta" />
                </collection>
            </param>
            <param name="criterion" value="N50"/>
            <output name="output" value="sample1.fasta" />
        </test>
    </tests>
    <help><![CDATA[
        Pick the best assembly from a collection of assemblies and a combined QUAST report.
    ]]></help>
</tool>