<macros>
    <!--
    This is the TEMPLATE macro for MultiQC
    1. please copy this template_plugin.xml to your own file e.g. trimmomatic_plugin.xml
    2. Replace `TEMPLATE` with the name of the plugin, e.g. `fastqc`. The tokens and xml-names need to be called `trimmomatic_form` or `TRIMMOMATIC_COMMAND`
    3. import your new *_plugin.xml macro into the main multiqc.xml file at the top of the file
    4. add a new option to the main select element, e.g. `<option value="trimmomatic">Trimmomatic</option>`
    5. add the *_COMMAND token to the <command> section.
    6. add the *_test macro to the test section.
    7. remove all unused comments from your new file
-->
    <token name="@TEMPLATE_COMMAND@"><![CDATA[
        <!--This pattern is used to check the file content in the @CHECK_LN_FILE@ token. The pattern should be included in the file. -->
        #set $pattern = "Trimmomatic"
        @LN_FILES@f
    ]]></token>
    <xml name="TEMPLATE_form">
        <!-- Please add here your input forms specific to your plugin. Keep the name as `input` if you have a single input.
            If you have multiple inputs have a look at other plugins, e.g. fastqc 
        -->
        <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="TEMPLATE_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="trimmomatic"/>
                    <param name="input" value="trimmomatic.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="cutadapt_trimmed_sequences_plot"/>
                    <has_text text="All-in-one FASTQ preprocessor"/>
                    <has_text text="trimmomatic_plot"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="dataset_33"/>
                    <has_text text="R1_fq"/>
                    <has_text text="result_right"/>
                    <has_text text="25839_merged"/>
                    <has_text text="C2"/>
                    <has_n_lines n="11"/>
                    <has_n_columns n="22"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="29"/>
        </test>
    </xml>
</macros>