<tool id="samtools_flagstat" name="Flagstat" version="2.0">
  <description>tabulate descriptive stats for BAM datset</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio"></expand>
  <expand macro="version_command"></expand>
  <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="samtools_flagstat_input1.bam" ftype="bam" />
      <output name="output1" file="samtools_flagstat_out1.txt" />
    </test>
  </tests>
  <help>

**What it does**

Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::

  200 + 0 in total (QC-passed reads + QC-failed reads)  
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  25 + 0 mapped (12.50%:nan%)
  200 + 0 paired in sequencing
  100 + 0 read1
  100 + 0 read2
  0 + 0 properly paired (0.00%:nan%)
  0 + 0 with itself and mate mapped
  25 + 0 singletons (12.50%:nan%)
  0 + 0 with mate mapped to a different chr
  0 + 0 with mate mapped to a different chr (mapQ>=5)
  
  </help>
  <expand macro="citations"></expand>
</tool>