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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 <requirement type="package" version="1.4.1">samtools</requirement>
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9 </requirements>
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10 <description>simple stats on BAM file</description>
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11 <stdio>
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12 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
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13 </stdio>
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14 <command><![CDATA[ Rscript '${__tool_directory__}/tool_template_render.R'
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15 -e $echo
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16 -b $input_bam
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17 -r $report
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18 -d $report.files_path
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19 -s $sink_message
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20 -t '${__tool_directory__}/tool_template.Rmd'
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21 ]]></command>
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22 <inputs>
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23 <param type="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
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24 <param type="data" name="input_bam" label="BAM file" optional="False"/>
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25 </inputs>
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26 <outputs>
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27 <data name="report" format="html" label="tool name report" hidden="false"/>
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28 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
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29 </outputs>
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30 <help><![CDATA[<code>samtools flagstat in.sam|in.bam|in.cram</code>
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31
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32 Does a full pass through the input file to calculate and print statistics to stdout]]></help>
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33 <citations>
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34 <citation><![CDATA[
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35 @article{allaire2016rmarkdown,
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36 title={rmarkdown: Dynamic Documents for R, 2016},
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37 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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38 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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39 journal={R package version 0.9},
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40 volume={6},
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41 year={2016}
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42 ]]></citation>
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43 <citation type="bibtex"><![CDATA[@article{li2009sequence,
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44 title={The sequence alignment/map format and SAMtools},
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45 author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
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46 journal={Bioinformatics},
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47 volume={25},
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48 number={16},
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49 pages={2078--2079},
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50 year={2009},
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51 publisher={Oxford University Press}
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52 }]]></citation>
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53 </citations>
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54 </tool>
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