<macros>
    <token name="@BISMARK_COMMAND@"><![CDATA[
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            @CREATE_REPEAT_DIR_1@
            #if str($repeat2.type) == "align"
                #for $file in $repeat2.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "dedup"
                #for $file in $repeat2.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "meth_extract"
                #for $file in $repeat2.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "m_bias"
                #for $file in $repeat2.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #elif str($repeat2.type) == "bam2nuc"
                #for $file in $repeat2.input
                    @ESCAPE_IDENTIFIER@
                    #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt')
                    ln -s '$file' '$file_path' &&
                #end for
            #end if
        #end for
    ]]></token>
    <xml name="bismark_form">
        <repeat name="output" title="Bismark output" min="1">
            <param name="type" type="select" label="Type of Bismark output?">
                <option value="align">Alignment file</option>
                <option value="dedup">Deduplication file</option>
                <option value="meth_extract">Methylation file</option>
                <option value="m_bias">m_bias file</option>
                <option value="bam2nuc">bam2nuc file</option>
            </param>
            <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
        </repeat>
    </xml>
    <!-- add here your test files and tests, the more stringent the better -->
    <xml name="bismark_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bismark"/>
                    <repeat name="output">
                        <param name="type" value="align"/>
                        <param name="input" value="bismark.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="bismark-alignment"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="bismark_txt_SE_report"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="0"/>
        </test>
    </xml>
</macros>