<tool id="rmarkdown_samtools_flagstat" name="R Markdown samtools flagstat" version="1.0.0">
  <requirements>
    <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
    <requirement type="package" version="1.20.0">r-getopt</requirement>
    <requirement type="package" version="1.3">r-rmarkdown</requirement>
    <requirement type="package" version="0.3.5">r-htmltools</requirement>
    <requirement type="package" version="0.5.0">r-dplyr</requirement>
    <requirement type="package" version="1.4.1">samtools</requirement>
  </requirements>
  <description>simple stats on BAM file</description>
  <stdio>
    <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
  </stdio>
  <command><![CDATA[                    Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R'
                        -e $echo
                        -b '$input_bam'
                        -n '$input_bam.name'
                        -r $report
                        -d $report.files_path
                        -s $sink_message
                        -t '${__tool_directory__}/rmarkdown_samtools_flagstat.Rmd'
                    ]]></command>
  <inputs>
    <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
    <param type="data" format="bam,sam" name="input_bam" label="BAM/SAM file" optional="False"/>
  </inputs>
  <outputs>
    <data name="report" format="html" label="rmarkdown flagstat report" hidden="false"/>
    <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
  </outputs>
  <help><![CDATA[
  samtools flagstat in.sam|in.bam|in.cram

Does a full pass through the input file to calculate and print statistics to stdout]]></help>
  <citations>
    <citation type="bibtex"><![CDATA[
                    @article{allaire2016rmarkdown,
                        title={rmarkdown: Dynamic Documents for R, 2016},
                        author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
                        and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
                        journal={R package version 0.9},
                        volume={6},
                        year={2016}
                    }]]></citation>
    <citation type="bibtex"><![CDATA[@article{li2009sequence,
  title={The sequence alignment/map format and SAMtools},
  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},
  journal={Bioinformatics},
  volume={25},
  number={16},
  pages={2078--2079},
  year={2009},
  publisher={Oxford University Press}
}]]></citation>
  </citations>
</tool>