/tools/samtools/samtools_flagstat.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 29 lines · 25 code · 4 blank · 0 comment · 0 complexity · 01cd42218f46a97a1f53f3392bee37fc MD5 · raw file
- <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>