<tool id="beacon2_runs" name="Beacon2 Runs" version="1.0.0" profile="21.05">
    <description>Query the runs collection in the beacon database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        beacon2-search runs
        --db-host '$db_host'
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        #if str($advanced_settings.identification)
            --identification '$advanced_settings.identification'
        #end if
        #if str($advanced_settings.individualId)
            --individualId '$advanced_settings.individualId'
        #end if
        #if str($advanced_settings.libraryLayout)
            --libraryLayout '$advanced_settings.libraryLayout'
        #end if
        #if str($advanced_settings.librarySelection)
            --librarySelection '$advanced_settings.librarySelection'
        #end if
        #if str($advanced_settings.librarySource)
            --librarySource '$advanced_settings.librarySource'
        #end if
        #if str($advanced_settings.libraryStrategy)
            --libraryStrategy '$advanced_settings.libraryStrategy'
        #end if
        #if str($advanced_settings.platform)
            --platform '$advanced_settings.platform'
        #end if
        #if str($advanced_settings.platformModel)
            --platformModel '$advanced_settings.platformModel'
        #end if
        #if str($advanced_settings.runDate)
            --runDate '$advanced_settings.runDate'
        #end if
        > runs_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="--identification" optional="true" type="text" label="ID" value="" help="Run ID" />
            <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="Reference to the individual ID, e.g. TCGA-AO-A0JJ" />
            <param argument="--libraryLayout" optional="true" type="text" label="LIBRARY LAYOUT" value="" help="Ontology value for the library layout e.g 'PAIRED', 'SINGLE'" />
            <param argument="--librarySelection" optional="true" type="text" label="LIBRARY SELECTION" value="" help="Selection method for library preparation, e.g 'RANDOM', 'RT-PCR'" />
            <param argument="--librarySource" optional="true" type="text" label="LIBRARY SOURCE" value="" help="Ontology value for the source of the sequencing or hybridization library, e.g 'genomic source', 'transcriptomic source'" />
            <param argument="--libraryStrategy" optional="true" type="text" label="LIBRARY STRATEGY" value="" help="Library strategy, e.g. 'WGS'" />
            <param argument="--platform" optional="true" type="text" label="PLATFORM" value="" help="General platform technology label where the specific model is not relevant, e.g. Illumina" />
            <param argument="--platformModel" optional="true" type="text" label="PLATFORM MODEL" value="" help="Ontology value for experimental platform or methodology used, e.g. 'Illumina HiSeq 3000'" />
            <param argument="--runDate" optional="true" type="text" label="RUN DATE" value="" help="Date at which the experiment was performed" />
        </section>
    </inputs>
    <outputs>
        <data name="out_runs_query" format="json" label="${tool.name} on ${on_string}: Runs Query" from_work_dir="runs_query_findings.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="database" value="beacon" />
            <param name="collection" value="test" />
            <param name="db_host" value="20.108.51.167" />
            <param name="platform" value="Illumina " />
            <param name="platformModel" value="2017-04-30" />
            <param name="librarySource" value="KAPA library quantification kit" />
            <param name="libraryLayout" value="PAIRED" />
            <output name="out_runs_query">
                <assert_contents>
                    <has_text_matching expression="_id"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Beacon2 Runs queries the runs collection in the Beacon database for details on procedures used for sequencing a biosample. 
    ]]></help>
    <expand macro="citations" />
</tool>