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1 <tool id="aurora_data" name="aurora_data" version="1.0.0">
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2 <description>Collect data for other aurora galaxy tools.</description>
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3 <requirements>
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4 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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7 </requirements>
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8 <stdio>
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9 <regex match="XXX" source="stderr" level="warning"
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10 description="Check the warnings_and_errors.txt file for more details."/>
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11 </stdio>
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12 <command><![CDATA[
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13 export TOOL_DIR='${__tool_directory__}' &&
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14
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15 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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16
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17 -o $report
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18 -d $report.files_path
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19
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20 ]]></command>
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21 <inputs>
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22 <repeat name="data_repeat" title="data" min="1" default="1">
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23 <param type="data" name="data" label="Data from history" optional="False"/>
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24 <param type="text" name="data_name" label="data name" optional="False" help="data name has to be unique."/>
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25 </repeat>
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26 </inputs>
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27 <outputs>
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28 <data name="report" format="html" label="${tool.name} on ${on_string}" hidden="false"/>
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29 </outputs>
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30 <citations>
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31 <citation type="bibtex"><![CDATA[
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32 @article{allaire2016rmarkdown,
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33 title={rmarkdown: Dynamic Documents for R, 2016},
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34 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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35 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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36 journal={R package version 0.9},
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37 volume={6},
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38 year={2016}
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39 }
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40 ]]></citation>
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41 <citation type="bibtex"><![CDATA[
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42 @book{xie2015dynamic,
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43 title={Dynamic Documents with R and knitr},
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44 author={Xie, Yihui},
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45 volume={29},
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46 year={2015},
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47 publisher={CRC Press}
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48 }
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49 ]]></citation>
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50 </citations>
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51 </tool>
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