mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
30 lines
798 B
XML
30 lines
798 B
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="3.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>
|