<tool id="beacon2_bracket" name="Beacon2 Bracket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Specifies a sequence ranges for both the start and end positions of a genomic variation</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[    
        beacon2-search bracket
        --db-host '$db_host'
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        --start-minimum $start_minimum
        --start-maximum $start_maximum
        --end-minimum $end_minimum
        --end-maximum $end_maximum
        #if str($advanced_settings.variantType)
            --variantType '$advanced_settings.variantType'
        #end if
        #if str($advanced_settings.referenceName)
            --referenceName '$advanced_settings.referenceName'
        #end if
        > bracket_query_findings.json
    ]]></command>
    <expand macro="configfile"/>
    <inputs>
        <expand macro="Connection_to_MongoDB" />
        <expand macro="Database_Configuration" />
        <param argument="--start-minimum" type="integer" label="Start minimum position" value="" help="" />
        <param argument="--start-maximum" type="integer" label="Start maximum position" value="" help="" />
        <param argument="--end-minimum" type="integer" label="End minimum position" value="" help="" />
        <param argument="--end-maximum" type="integer" label="End maximum position" value="" help="" />
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <param argument="--referenceName" optional="true" type="text" label="Reference Name" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
            <param argument="--variantType"  optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
        </section>
    </inputs>
    <outputs>
        <data name="out_bracket_query" format="json" label="${tool.name} on ${on_string}: Bracket Query" from_work_dir="bracket_query_findings.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="database" value="beacon" />
            <param name="collection" value="genomicVariations" />
            <param name="db_host" value="20.108.51.167" />
            <param name="start_minimum" value="131836" />
            <param name="start_maximum" value="161836" />
            <param name="end_minimum" value="131837" />
            <param name="end_maximum" value="151837" />
            <param name="variantType" value="SNP" />
            <output name="out_bracket_query">
                <assert_contents><has_text_matching expression="_id"/></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Bracket Queries allow the specification of sequence ranges for both start and end positions of a genomic variation. The typical example here is the query for similar structural variants - particularly CNVs - affecting a genomic region but potentially differing in their exact base extents.
    ]]></help>
    <expand macro="citations" />
</tool>