<tool id="beacon2_datasets" name="Beacon2 Datasets" version="1.0.0" profile="21.05">
    <description>Query the datasets collection in the beacon database groupings of variants or individuals who belong to the same repository</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        beacon2-search datasets
        --db-host '$db_host'
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        #if str($advanced_settings.dataUseConditions)
            --dataUseConditions '$advanced_settings.dataUseConditions'
        #end if
        #if str($advanced_settings.ontologyModifiers)
            --ontologyModifiers '$advanced_settings.ontologyModifiers'
        #end if
        #if str($advanced_settings.identification)
            --identification '$advanced_settings.identification'
        #end if
        #if str($advanced_settings.name)
            --name '$advanced_settings.name'
        #end if
        > datasets_query_findings.json
        ]]>
    </command>
    <expand macro="configfile"/>
    <inputs>
        <expand macro="Connection_to_MongoDB"/>
        <expand macro="Database_Configuration"/>
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <param argument="--dataUseConditions" optional="true" type="text" label="DATAUSECONDITIONS" value="" help="Data use conditions applying to this dataset, e.g. disease specific research" />
            <param argument="--ontologyModifiers" optional="true" type="text" label="DATA USE CONDITIONS MODIFIERS" value="" help="Modifiers that further specify the datasets, e.g. coronary artery disease" />
            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Unique identifier of the dataset" />
            <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the dataset" />
        </section>
    </inputs>
    <outputs>
        <data name="out_datasets_query" format="json" label="${tool.name} on ${on_string}: Datasets Query" from_work_dir="datasets_query_findings.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="database" value="beacon" />
            <param name="collection" value="datasets" />
            <param name="db_host" value="20.108.51.167" />
            <param name="identification" value="refvar-668fcf57aee552bc911b966e" />
            <param name="name" value="The Genome in a Bottle Consortium (GIAB)" />
            <output name="out_datasets_query">
                <assert_contents>
                    <has_text_matching expression="_id"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Beacon2 Datasets queries the datasets collection in the Beacon database to study the variants or individuals in a populations or groups who belong to the same repository.
    ]]></help>
    <expand macro="citations" />
</tool>