<?xml version="1.0" ?>
<macros>
    <token name="@VERSION@">2.1b</token>
    <xml name="db_prep">
        <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
        <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
    </xml>
    <xml name="output_alignments">
        <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
        <conditional name="blast">
            <param name="blast_output" type="select" label="Output BLAST report?">
                <option value="True">Yes</option>
                <option value="False" selected="True">No</option>
            </param>
            <when value="True">
                <param name="blast_format" type="select" label="BLAST-like format?">
                    <option value="0">pairwise (--blast '0')</option>
                    <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
                    <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
                    <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
                    <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
                </param>
            </when>
            <when value="False"/>
        </conditional>
    </xml>
    <token name="@ALIGNMENTS@">
        $report.print_all_reads
        --sam
        --SQ
        #if $report.blast.blast_output == 'True'
            --blast '$report.blast.blast_format'
        #end if
    </token>
</macros>