<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.22.1" profile="17.01">
    <description>Generates a graphical HTML report page from report outputs of Bismark</description>
    <requirements>
        <requirement type="package" version="0.22.1">bismark</requirement>
        <requirement type="package" version="1.8">samtools</requirement>
        <requirement type="package" version="2.3.5">bowtie2</requirement>
    </requirements>
    <command><![CDATA[
        python '$__tool_directory__/bismark2report_wrapper.py'

        --alignment_report '$alignment'

        #if $additional_reports['dedup']:
        	--dedup_report '$additional_reports["dedup"]'
        #end if
        #if $additional_reports['splitting']:
            --splitting_report '$additional_reports["splitting"]'
        #end if
        #if $additional_reports['mbias']:
            --mbias_report '$additional_reports["mbias"]'
        #end if
        #if $additional_reports['nucleotide']:
            --nucleotide_report '$additional_reports["nucleotide"]'
        #end if

        --output_html_report '$output_html_report'

        #if $separate_logfile:
            --log_report '$log_report'
        #end if
]]>
    </command>

    <inputs>
        <param name="alignment" type="data" format="txt" label="Submit a Bismark mapping report" optional="False"/>
        <section name="additional_reports" title="Additional reports to include in the HTML page (optional)"
                 expanded="True">
            <param name="dedup" type="data" format="txt" label="Submit the corresponding Bismark deduplication report"
                   optional="True" help="Optional output of the module *Bismark Deduplicate*"/>
            <param name="splitting" type="data" format="txt" label="Submit the corresponding Bismark splitting report"
                   optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
            <param name="mbias" type="data" format="txt" label="Submit the corresponding Bismark M-bias report"
                   optional="True" help="Optional output of the module *Bismark Methylation Extractor*"/>
            <param name="nucleotide" type="data" format="txt" label="Submit the corresponding Bismark nucleotide report"
                   optional="True" help="Optional output of the module *Bismark Mapping*"/>
        </section>
        <param name="separate_logfile" type="boolean" truevalue="true" falsevalue="false" checked="False"
               label="Create a separate logfile, otherwise logs are added to the dataset info."/>
    </inputs>

    <outputs>
        <data name="output_html_report" format="html"
              label="${tool.name} on ${on_string}: Download pretty html report"/>
        <data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)">
            <filter>( separate_logfile is True )</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="alignment" value="mapping_report.txt" ftype="txt"/>
            <param name="dedup" value="dedup_report.txt" ftype="txt"/>
            <param name="splitting" value="output_splitting_report.txt" ftype="txt"/>
            <param name="mbias" value="output_mbias_report.txt" ftype="txt"/>
            <output name="output_html_report" file="output_html_report.html" ftype="html" lines_diff="8"/>
        </test>
    </tests>

    <help>
        <![CDATA[
**What it does**

    | This tool uses a Bismark alignment report to generate a graphical HTML report page.
    | Optionally, further reports of the Bismark suite such as deduplication, methylation extractor splitting or M-bias reports can be specified as well.

]]>
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btr167</citation>
    </citations>
</tool>