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1 <tool id="rmarkdown_samtools_flagstat" name="R Markdown samtools flagstat" 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__}/rmarkdown_samtools_flagstat_render.R'
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15 -e $echo
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16 -b $input_bam
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17 -n $input_bam.name
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18 -r $report
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19 -d $report.files_path
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20 -s $sink_message
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21 -t '${__tool_directory__}/rmarkdown_samtools_flagstat.Rmd'
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22 ]]></command>
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23 <inputs>
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24 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
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25 <param type="data" name="input_bam" label="BAM file" optional="False"/>
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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 report" hidden="false"/>
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29 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
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30 </outputs>
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31 <help><![CDATA[<code>samtools flagstat in.sam|in.bam|in.cram</code>
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32
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33 Does a full pass through the input file to calculate and print statistics to stdout]]></help>
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34 <citations>
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35 <citation><![CDATA[
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36 @article{allaire2016rmarkdown,
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37 title={rmarkdown: Dynamic Documents for R, 2016},
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38 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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39 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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40 journal={R package version 0.9},
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41 volume={6},
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42 year={2016}
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43 ]]></citation>
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44 <citation type="bibtex"><![CDATA[@article{li2009sequence,
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45 title={The sequence alignment/map format and SAMtools},
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46 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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47 journal={Bioinformatics},
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48 volume={25},
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49 number={16},
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50 pages={2078--2079},
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51 year={2009},
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52 publisher={Oxford University Press}
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53 }]]></citation>
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54 </citations>
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55 </tool>
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