<macros>
    <token name="@FASTP_COMMAND@"><![CDATA[
        #set $pattern = "report_title"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
            ln -s '$file' '$file_path' &&
            grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
        #end for
    ]]></token>
    <xml name="fastp_form">
        <param name="input" type="data" format="json" label="Output of fastp" help="It should be the json report from fastp containing 'report_title" multiple="true"/>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="fastp_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="fastp"/>
                    <param name="input" value="fastp1.json.txt,fastp2.json.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="All-in-one FASTQ preprocessor"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="fastp_mqc_generalstats_fastp_pct_duplication"/>
                    <has_text text="R1_fq"/>
                    <has_text text="fastp_mqc_generalstats_fastp_after_filtering_q30_rate"/>
                    <has_text text="bwa-mem-fastq1_fq"/>
                    <has_n_lines n="3"/>
                    <has_n_columns n="8"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="15"/>
        </test>
    </xml>
</macros>