<macros>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@TOOL_VERSION@">2.1.1</token>
    <xml name="reference_interface">
        <conditional name="reference_source">
            <param name="ref_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param argument="--ref" type="select" label="Reference genome">
                    <options from_data_table="fasta_indexes">
                        <!-- <filter type="data_meta" column="dbkey" key="dbkey" ref="input_sample_file" /> -->
                        <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" />
            </when>
        </conditional>
    </xml>
    <xml name="adv_shared_1">
        <param name="batches" type="integer" value="10000000" min="0" label="Batches" help="Batch of genome segmentation interval." />
        <param name="max_split_parts" type="integer" value="7" min="0" label="Maximum number of split segments" help="Maximum number of split segments a read may be aligned before it is ignored." />
        <param name="min_mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Minimum mapping quality value of alignment to be taken into account." />
        <param name="min_read_len" type="integer" value="500" min="0" label="Minimum read length" help="Ignores reads that only report alignments with not longer than bp." />
        <param name="merge_del_threshold" type="integer" value="0" min="0" label="Maximum distance of deletions" help="Maximum distance of deletion signals to be merged." />
        <param name="merge_ins_threshold" type="integer" value="100" min="0" label="Maximum distance of insertions" help="Maximum distance of insertion signals to be merged." />
        <param name="min_support" type="integer" value="10" min="0" label="Minimum number of reads that support a SV" help="Minimum number of reads that support a SV to be reported." />
        <param name="min_size" type="integer" value="30" min="0" label="Minimum SV length" help="Minimum length of SV to be reported. " />
        <param name="max_size" type="integer" value="100000" min="0" label="Maximum SV length" help="Maximum length of SV to be reported." />
        <section name="genotyping" title="Genotyping settings" expanded="false">
            <param name="genotype" type="boolean" checked="False" label="Genotype" help="Enable to generate genotypes." />
            <param name="gt_round" type="integer" value="500" min="1" label="Maximum iterations for genotyping" help="Maximum round of iteration for alignments searching if perform genotyping." />
        </section>
    </xml>
    <xml name="adv_pb_clr">
        <section name="seq_method" title="PacBio CLR settings" expanded="false">
            <param name="max_cluster_bias_INS" type="integer" value="100" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." />
            <param name="diff_ratio_merging_INS" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." />
            <param name="max_cluster_bias_DEL" type="integer" value="200" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." />
            <param name="diff_ratio_merging_DEL" type="float" value="0.5" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." />
        </section>
    </xml>
    <xml name="adv_pb_ccs">
        <section name="seq_method" title="PacBio CCS(HIFI) settings" expanded="false">
            <param name="max_cluster_bias_INS" type="integer" value="1000" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." />
            <param name="diff_ratio_merging_INS" type="float" value="0.9" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." />
            <param name="max_cluster_bias_DEL" type="integer" value="1000" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." />
            <param name="diff_ratio_merging_DEL" type="float" value="0.5" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." />
        </section>
    </xml>
    <xml name="adv_ont">
        <section name="seq_method" title="ONT settings" expanded="false">
            <param name="max_cluster_bias_INS" type="integer" value="100" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." />
            <param name="diff_ratio_merging_INS" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." />
            <param name="max_cluster_bias_DEL" type="integer" value="100" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." />
            <param name="diff_ratio_merging_DEL" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." />
        </section>
    </xml>
    <xml name="adv_other">
        <section name="seq_method" title="Advanced method settings" expanded="true">
            <param name="max_cluster_bias_INS" type="integer" value="100" min="0" label="Maximum cluster distance (insertion)" help="Maximum distance to cluster read together for insertion." />
            <param name="diff_ratio_merging_INS" type="float" value="0.3" min="0" max="1" label="Breakpoints merge threshold (insertion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for insertion." />
            <param name="max_cluster_bias_DEL" type="integer" value="200" min="0" label="Maximum cluster distance (deletion)" help="Maximum distance to cluster read together for deletion." />
            <param name="diff_ratio_merging_DEL" type="float" value="0.5" min="0" max="1" label="Breakpoints merge threshold (deletion)" help="Do not merge breakpoints with basepair identity more than the ratio of default for deletion." />
        </section>
    </xml>
    <xml name="adv_shared_2">
        <param name="max_cluster_bias_INV" type="integer" value="500" min="0" label="Maximum distance to cluster (inversion)" help="Maximum distance to cluster read together for inversion." />
        <param name="max_cluster_bias_DUP" type="integer" value="500" min="0" label="Maximum distance to cluster (duplication)" help="Maximum distance to cluster read together for duplication." />
        <param name="max_cluster_bias_TRA" type="integer" value="50" min="0" label="Maximum distance to cluster (translocation)" help="Maximum distance to cluster read together for translocation." />
        <param name="diff_ratio_filtering_TRA" type="float" value="0.6" min="0" max="1" label="Breakpoints filter threshold (translocation)" help="Filter breakpoints with basepair identity less than the ratio of default for translocation." />
        <param name="report_readid" type="boolean" checked="False" label="Report read id" help="Enable to report supporting read ids for each SV." />
    </xml>
</macros>