<macros>
    <token name="@TOOL_VERSION@">5.3.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.02</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">quast</requirement>
            <requirement type="package" version="0.7.18">bwa</requirement>
            <requirement type="package" version="2.31.1">bedtools</requirement>
            <requirement type="package" version="2.76">perl-gd</requirement>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">quast</xref>
        </xrefs>
    </xml>
    <xml name="gene_thresholds">
        <param argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bty266</citation>
            <citation type="doi">10.1093/bioinformatics/btw379</citation>
            <citation type="doi">10.1093/bioinformatics/btv697</citation>
            <citation type="doi">10.1093/bioinformatics/btt086</citation>
        </citations>
    </xml>
    <xml name="min_identity_macros" token_value="">
        <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/>
    </xml>
    <xml name="custom">
        <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs">
            <option value="true">Yes, specify custom names</option>
            <option value="false" selected="true">No, use dataset names</option>
        </param>
    </xml>
    <xml name="labelled_input">
        <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/>
        <param argument="--labels" type="text" value="" label="Name"/>
    </xml>
    <xml name="reads_option">
        <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads.">
            <option value="disabled">Disabled</option>
            <option value="single">Illumina single-end reads</option>
            <option value="paired">Illumina paired-end reads</option>
            <option value="paired_collection">Illumina paired-end reads in paired collection</option>
            <option value="paired_interlaced">Illumina interlaced paired-end reads</option>
            <option value="mate_paired">Illumina mate-pair reads</option>
            <option value="pacbio">Pacbio SMRT reads</option>
            <option value="nanopore">Nanopore reads</option>
        </param>
    </xml>
</macros>