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1 <tool id="rmarkdown_merge_rmarkdown" name="Merge R Markdown" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
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5 <requirement type="package" version="1.3">r-rmarkdown</requirement>
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6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
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8 </requirements>
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9 <description>Merge multiple R Markdown files to generate one single report</description>
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10 <stdio>
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11 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
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12 </stdio>
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1
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13 <command><![CDATA[ Rscript '${__tool_directory__}/rmarkdown_merge_rmarkdown_render.R'
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14 -e $echo
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15 -r $report
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16 -d $report.files_path
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17 -s $sink_message
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18 -t '${__tool_directory__}/rmarkdown_merge_rmarkdown.Rmd'
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19 ]]></command>
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20 <inputs>
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1
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21 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
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22 <param type="data" name="rmarkdown_files" label="R Markdown files" optional="False" format="Rmd" multiple="True"/>
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23 </inputs>
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24 <outputs>
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25 <data name="report" format="html" label="tool name report" hidden="false"/>
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26 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
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27 </outputs>
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28 <help><![CDATA[some help text]]></help>
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29 <citations>
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30 <citation><![CDATA[
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31 @article{allaire2016rmarkdown,
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32 title={rmarkdown: Dynamic Documents for R, 2016},
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33 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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34 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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35 journal={R package version 0.9},
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36 volume={6},
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37 year={2016}
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38 ]]></citation>
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39 </citations>
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40 </tool>
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