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<tool id="bgzip" name="bgzip" version="0.0.1">
    <description>Block compression/decompression utility. Required for use of tabix.</description>
    <requirements>
        <requirement type="package" version="0.2.6">tabix</requirement>
    </requirements>
    <command>
        bgzip 

        #if str($virtualOffset) != ""
            -b $virtualOffset
        #end if

        #if str($size) != ""
            -s $size
        #end if

        $input
    </command>
    <inputs>
        <param name="input" type="data" label="Input file" />
        <param name="virtualOffset" type="text" optional="yes" label="Virtual Offset" />
        <param name="size" type="text" optional="yes" label="Size" />
    </inputs>

    <outputs>
        <data format= "bgz" name="output" from_work_dir="${input.file_name}.bgz"/>
    </outputs>

    <help>
**What it does:** 

The input data file is sorted and compressed by bgzip which has a gzip(1) like interface. Tabix requires the file to be compressed using this tool first.

**Citation:**

Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.

http://samtools.sourceforge.net/tabix.shtml

**Example:**

(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;

tabix -p gff sorted.gff.gz;

tabix sorted.gff.gz chr1:10,000,000-20,000,000;

    </help>
</tool>