<macros>
<token name="@FASTQC_COMMAND@"><![CDATA[
    #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
        @CREATE_REPEAT_DIR_1@
        #if str($repeat2.type) == "data"
            #for $k, $file in enumerate($repeat2.input)
                #set file_dir = os.path.join($repeat_dir, 'file_' + str($k))
                #set file_path = os.path.join($file_dir, 'fastqc_data.txt')
                mkdir '$file_dir' &&
                ln -s '$file' '$file_path' &&
            #end for
        #elif str($repeat2.type) == "theoretical_gc"
            #for $file in $repeat2.input
                @ESCAPE_IDENTIFIER@
                #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc')
                ln -s '$file' '$file_path' &&
            #end for
        #end if
    #end for
]]></token>

<xml name="fastqc_form">
    <repeat name="output" title="FastQC output" min="1">
        <param name="type" type="select" label="Type of FastQC output?">
            <option value="data">Raw data</option>
            <option value="theoretical_gc">Theorectical GC</option>
        </param>
        <param name="input" type="data" format="txt" multiple="true" label="FastQC output">
            <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator>
        </param>
    </repeat>
</xml>

<!-- add here your test files and tests, the more stringent the better -->
<xml name="fastqc_test">
    <test expect_num_outputs="3">
        <repeat name="results">
            <conditional name="software_cond">
                <param name="software" value="fastqc" />
                <repeat name="output">
                    <param name="type" value="data"/>
                    <param name="input" value="fastqc_1.txt,fastqc_2.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="fastqc_seq_heatmap_key_t" />
            </assert_contents>
        </output>
        <output name="stats">
            <assert_contents>
                <has_text text="poulet5_1"/>
                <has_text text="poulet5_2"/>
                <has_text text="FastQC_mqc_generalstats_fastqc_median_sequence_length"/>
                <has_n_lines n="3"/>
                <has_n_columns n="7"/>
            </assert_contents>
        </output>
        <output_collection name="plots" type="list" count="7"/>
    </test>
</xml>


</macros>