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1 <tool id="tool_template" name="tool name" 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>some descriptions about the tool.</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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2
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13 <command><![CDATA[ Rscript '${__tool_directory__}/tool_template_render.R'
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14 -e $echo
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15 -i $input_txt
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16 -r $report
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17 -d $report.files_path
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18 -s $sink_message
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19 -t '${__tool_directory__}/tool_template.Rmd'
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20 ]]></command>
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21 <inputs>
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22 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
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2
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23 <param type="data" name="input_txt" optional="False" format="txt"/>
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24 </inputs>
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25 <outputs>
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26 <data name="report" format="html" label="tool name report" hidden="false"/>
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27 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
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28 </outputs>
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29 <help><![CDATA[some help text]]></help>
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30 <citations>
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1
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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 ]]></citation>
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40 </citations>
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41 </tool>
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