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  2. galaxy-central (ngs)

Source

galaxy-central (ngs) / tools / samtools / samtools_flagstat.xml

<tool id="samtools_flagstat" name="flagstat" version="1.0.0">
  <requirements>
    <requirement type="package">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

  </help>
</tool>