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author devteam
date Tue, 20 Aug 2013 12:33:44 -0400
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1 <tool id="samtools_flagstat" name="flagstat" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="0.1.18">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
24 This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
25
26 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
27
28 ------
29
30 **Citation**
31
32 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
33
34 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
35
36 </help>
37 </tool>