<tool id="BCF Tools Index" name="BCF Tools Index">
  <description>This tool allows the user to index sorted BCF for random access.</description>

  <requirements>
        <requirement type="package" version="0.1.18">samtools</requirement>
    </requirements>

  <command interpreter='python' >bcftools_wrapper.py bcftools index $input > $output </command>

  <inputs>
    <param  name="input" type="data" format="bcf" label="BCF File"/>
  </inputs>

  <outputs>
    <data format="bcf" name="output" label= "BCF index output"/>
  </outputs>

     <help>
**What it does:** 

This tool allows the user to index sorted BCF for random access using BCFtools index from the SAMtools set of utilities:

http://samtools.sourceforge.net/samtools.shtml#4

------

**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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_


If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert.  CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__

    .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html

Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.)

    </help>

</tool>