<macros>
    <token name="@TOOL_VERSION@">2.28</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="edam_ontology">
        <edam_topics>                                                                                  
            <edam_topic>topic_0102</edam_topic>
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0292</edam_operation>
        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">minimap2</requirement>
            <requirement type="package" version="1.19.2">samtools</requirement>
        </requirements>
    </xml>
    <xml name="pe_anaylsis_fixed_selector">
        <param name="analysis_type_selector" type="select"
        label="Presets for PE reads alignment"
        help="These are the minimap2 preset options for PE alignment of short reads. You can customize these and other settings in the indexing, mapping and alignment options sections below.">
            <option value="sr">Short reads without splicing (-k21 -w11 --sr -F800 -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20 -s40 -g200 -2K50m --heap-sort=yes --secondary=no) (sr)</option>
        </param>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btp324</citation>
            <citation type="doi">10.1093/bioinformatics/btp698</citation>
            <citation type="bibtex">@misc{1303.3997,
                Author = {Heng Li},
                Title = {Minimap2: fast pairwise alignment for long nucleotide sequences},
                Year = {2017},
                Eprint = {arXiv:1708.01492},
                url = {https://arxiv.org/abs/1708.01492},
                }</citation>
        </citations>
    </xml>
</macros>