<tool id="samtools_flagstat" name="flagstat" version="1.0.0">
  <requirements>
    <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <description>provides simple stats on BAM files</description>
  <command>samtools flagstat "$input1" > "$output1"
  </command>
  <inputs>
    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
  </inputs>
  <outputs>
    <data name="output1" format="txt" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="3unsorted.bam" ftype="bam" />
      <output name="output1" file="samtools_flagstat_out1.txt" />
    </test>
  </tests>
  <help>

**What it does**

This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.

.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml

------

**Citation**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_

If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

  </help>
</tool>