<tool id="rmarkdown_flagstat" name="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>Descriptive stats for BAM dataset</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__}/tool_template_render.R'
                        -e $echo
                        -r $report
                        -d $report.files_path
                        -s $sink_message
                        -t '${__tool_directory__}/tool_template.Rmd
                    ]]></command>
  <inputs>
    <param type="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
    <param type="data" name="input_bam" label="BAM file" optional="False" format="bam"/>
  </inputs>
  <outputs>
    <data name="report" format="html" label="tool name 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[Provides counts for each of 13 categories based primarily on bit flags in the FLAG field. Each category in the output is broken down into QC pass and QC fail, which is presented as "#PASS + #FAIL" followed by a description of the category.]]></help>
  <citations>
    <citation><![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>