view aurora_data.xml @ 0:ebb7afcb2b75 draft default tip

planemo upload

<tool id="aurora_data" name="aurora_data" version="1.0.0">
    <description>Collect data for other aurora galaxy tools.</description>
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[
        export TOOL_DIR='${__tool_directory__}' &&

        Rscript '${__tool_directory__}/rmarkdown_report_render.R'

			-o $report
			-d $report.files_path
        
    ]]></command>
    <inputs>
        <repeat name="data_repeat" title="data" min="1" default="1">
            <param type="data" name="data" label="Data from history" optional="False"/>
            <param type="text" name="data_name" label="data name" optional="False" help="data name has to be unique."/>
        </repeat>
    </inputs>
    <outputs>
        <data name="report" format="html" label="${tool.name} on ${on_string}" hidden="false"/>
    </outputs>
    <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation>
        <citation type="bibtex"><![CDATA[
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation>
    </citations>
</tool>