Mercurial > repos > mingchen0919 > aurora_bdss_url

<tool name="aurora_bdss_url" id='aurora_bdss_url_report' version="1.0.0">
    <description>
        some description
    </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>
    <command><![CDATA[

        ######### each aurora tool generates a html file and have an files path directory associated with it.
        mkdir -p $report.files_path &&

        ######### three important paths:
        #########   1. path to tool installation directory
        #########   2. path to report html
        #########   3. path to files_path directory associated with the report output.
        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
        export REPORT='$report' &&
        export REPORT_FILES_PATH='$report.files_path' &&

        ############ create a hidden file to store r markdown rendering log
        touch $report.files_path/.r_rendering.log.txt &&

        ############ finally run the render.R script
        Rscript '${__tool_directory__}/rmarkdown_report_render.R'

            -o $report
            -d $report.files_path

            -u $urls


    ]]></command>
    <inputs>
        <param type="text" name="urls" area="true" size="5x25" label="data URLs"
               help="Multiple URLs should be separated with comma or space"/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="${tool.name} report"/>
        <data name="output" label="BDSS downloaded data">
            <discover_datasets pattern="__name_and_ext__" directory="download_dir" visible="true"/>
        </data>
    </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>
        <citation type="bibtex"><![CDATA[
            @online{jstree,
            author={Bozhanov, Ivan},
            year = 2018,
            url = {https://www.jstree.com/}
            }
        ]]></citation>
    </citations>
</tool>
author	mingchen0919
date	Tue, 12 Jun 2018 00:54:24 -0400
parents	0d15928a648c
children	2096940073af