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

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

**What it does**

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

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