<macros>
    <token name="@BBDUK_COMMAND@"><![CDATA[
        #set $pattern = "Executing jgi\.BBDuk"
        @LN_FILES@
    ]]></token>
    <xml name="bbduk_form">
        <param name="input" type="data" format="txt" multiple="true" label="Output of BBDuk" help="It should contain 'Executing jgi.BBDuk'"/>
    </xml>
    <xml name="bbduk_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bbduk"/>
                    <param name="input" value="bbduk.txt"/>
                </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="BBDuk"/>
                    <has_text text="BBDuk: Filtered Reads"/>
                    <has_text text="0.0"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="bbduk-Total_Removed_bases_percent"/>
                    <has_text text="bbduk-Total_Removed_bases"/>
                    <has_text text="bbduk-Total_Removed_reads_percent"/>
                    <has_text text="bbduk-Total_Removed_reads"/>
                    <has_text text="bbduk-Input_reads"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="6"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="2"/>
        </test>
    </xml>
</macros>