2
+ − 1 <tool id="rmarkdown_samtools_flagstat" name="R Markdown samtools flagstat" version="1.0.0">
+ − 2 <requirements>
+ − 3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+ − 4 <requirement type="package" version="1.20.0">r-getopt</requirement>
+ − 5 <requirement type="package" version="1.3">r-rmarkdown</requirement>
+ − 6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
+ − 7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
+ − 8 <requirement type="package" version="1.4.1">samtools</requirement>
+ − 9 </requirements>
+ − 10 <description>simple stats on BAM file</description>
+ − 11 <stdio>
+ − 12 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
+ − 13 </stdio>
+ − 14 <command><![CDATA[ Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R'
+ − 15 -e $echo
4
+ − 16 -b '$input_bam'
+ − 17 -n '$input_bam.name'
2
+ − 18 -r $report
+ − 19 -d $report.files_path
+ − 20 -s $sink_message
+ − 21 -t '${__tool_directory__}/rmarkdown_samtools_flagstat.Rmd'
+ − 22 ]]></command>
+ − 23 <inputs>
+ − 24 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
3
+ − 25 <param type="data" format="bam,sam" name="input_bam" label="BAM/SAM file" optional="False"/>
2
+ − 26 </inputs>
+ − 27 <outputs>
5
+ − 28 <data name="report" format="html" label="rmarkdown flagstat report" hidden="false"/>
2
+ − 29 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
+ − 30 </outputs>
3
+ − 31 <help><![CDATA[
+ − 32 samtools flagstat in.sam|in.bam|in.cram
2
+ − 33
+ − 34 Does a full pass through the input file to calculate and print statistics to stdout]]></help>
+ − 35 <citations>
3
+ − 36 <citation type="bibtex"><![CDATA[
2
+ − 37 @article{allaire2016rmarkdown,
+ − 38 title={rmarkdown: Dynamic Documents for R, 2016},
+ − 39 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+ − 40 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+ − 41 journal={R package version 0.9},
+ − 42 volume={6},
+ − 43 year={2016}
5
+ − 44 }]]></citation>
2
+ − 45 <citation type="bibtex"><![CDATA[@article{li2009sequence,
+ − 46 title={The sequence alignment/map format and SAMtools},
+ − 47 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},
+ − 48 journal={Bioinformatics},
+ − 49 volume={25},
+ − 50 number={16},
+ − 51 pages={2078--2079},
+ − 52 year={2009},
+ − 53 publisher={Oxford University Press}
+ − 54 }]]></citation>
+ − 55 </citations>
+ − 56 </tool>