<macros>
    <token name="@GATK_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            #if str($repeat2.type) == "varianteval"
                #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
                @LN_2_FILES@
            #elif str($repeat2.type) == "base_recalibrator"
                #set $pattern = "#:GATKTable:Arguments:Recalibration"
                @LN_2_FILES@
            #end if
        #end for
    ]]></token>
    <xml name="gatk_form">
        <repeat name="output" title="GATK output" min="1">
            <param name="type" type="select" label="Type of GATK output?">
                <option value="varianteval">Variant eval file</option>
                <option value="base_recalibrator">Base recalibrator file</option>
            </param>
            <param name="input" type="data" format="txt" multiple="true" label="GATK output"/>
        </repeat>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="gatk_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="gatk"/>
                    <repeat name="output">
                        <param name="type" value="base_recalibrator"/>
                        <param name="input" value="gatk_BaseRecalibrator.txt"/>
                    </repeat>
                    <repeat name="output">
                        <param name="type" value="varianteval"/>
                        <param name="input" value="gatk_varianteval.txt"/>
                    </repeat>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <param name="flat" value="true"/>
            <param name="export" value="true"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report"/>
                    <has_text text="Commment for the report"/>
                    <has_text text="gatk_varianteval_variant_plot"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="gatk_varianteval_txt"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="4"/>
        </test>
    </xml>
</macros>