/tools/samtools/samtools_flagstat.xml

 1<tool id="samtools_flagstat" name="flagstat" version="1.0.0">
 2  <requirements>
 3    <requirement type="package">samtools</requirement>
 4  </requirements>
 5  <description>provides simple stats on BAM files</description>
 6  <command>samtools flagstat "$input1" > "$output1"
 7  </command>
 8  <inputs>
 9    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
10  </inputs>
11  <outputs>
12    <data name="output1" format="txt" />
13  </outputs>
14  <tests>
15    <test>
16      <param name="input1" value="3unsorted.bam" ftype="bam" />
17      <output name="output1" file="samtools_flagstat_out1.txt" />
18    </test>
19  </tests>
20  <help>
21
22**What it does**
23
24This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
25
26.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
27
28  </help>
29</tool>