Mercurial > repos > devteam > samtools_flagstat
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author | devteam |
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date | Tue, 20 Aug 2013 12:33:44 -0400 |
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children | f92f13ccee76 |
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<tool id="samtools_flagstat" name="flagstat" version="1.0.0"> <requirements> <requirement type="package" version="0.1.18">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 ------ **Citation** 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. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> </tool>