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demo
author mingchen0919
date Mon, 12 Mar 2018 11:49:18 -0400
parents dd498df3f006
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<tool id="aurora_demo_site" name="Aurora Demo site" version="1.0.0">
    <description>A demo tool for demonstrating how Aurora Galaxy tool works. This tool is developed under the R Markdown
        framework and use shell, python and R script together to generate a random heatmap.
    </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>
        <requirement type="package" version="1.0.8">r-pheatmap</requirement>
    </requirements>
    <stdio>
        <regex match="XXX" source="stderr" level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command><![CDATA[Rscript '${__tool_directory__}/aurora_demo_site_render.R'

      -r $row_number
      -c $column_number

      -R $report
      -d $report.files_path
      -O $heatmap_data

      -T '${__tool_directory__}']]></command>
    <inputs>
        <param type="integer" name="row_number" label="Number of rows" optional="False" value="10"/>
        <param type="integer" name="column_number" label="Number of columns" optional="False" value="4"/>
    </inputs>
    <outputs>
        <data name="heatmap_data" format="tabular" hidden="false" label="aurora demo output"/>
        <data name="report" format="html" label="aurora demo site" 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>