annotate bismark_pretty_report/bismark2report_wrapper.xml @ 7:fcadce4d9a06 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'

<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.16.3">

    <description>Generates a graphical HTML report page from report outputs of Bismark</description>
    <!--<version_command>bismark version</version_command>-->

    <requirements>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>

    <command interpreter="python">
<![CDATA[
        bismark2report_wrapper.py

        --tool_dir "$__tool_directory__"

        --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 $output_html_report
        --output_html_report_link "$output_html_report_link"
        --output_dir "$output_html_report_link.files_path"

        ##--log_report $log_report
]]>
    </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>
    </inputs>

    <outputs>
        <!--<data name="output_html_report" format="html" label="${tool.name} on ${on_string}: Download pretty html report"/>-->
        <data name="output_html_report_link" format="html" label="${tool.name} on ${on_string}: Visualize pretty html report"/>
        <!--<data name="log_report" format="txt" label="${tool.name} on ${on_string}: log report (tool stdout)"/>-->
    </outputs>

    <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>