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planemo upload

Convert a BAM file into a BigWig coverage file. This can be used directly from
Galaxy for display at UCSC. The advantage over standard Wiggle format is that
the data is stored in a compressed format and can be retrieved by genome
region. This allows you to view regions of arbitrarily large Wiggle file data
at UCSC while avoiding the upload costs.

History
-------

v0.2.0 add a sort step after genomeCoverageBed which is required in some
instances otherwise bedGraphToBigWig will complain. This version also uses
Galaxy's dependency mechanism, added some tests, and updated some formatting.
By Lance Parsons.

v0.1.1 passes the forgotten split argument and moves to using the new
sub-command enabled bedtools. Thanks to David Leader.

As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using
genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to
be excluded from the coverage calculation, which is important for RNA-Seq.

Until v0.0.2, this Galaxy tool used the bam_to_wiggle.py script from
https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
which internally used pysam (and thus samtools) and wigToBigWig from UCSC.

Requirements
------------

If you are installing this tool manually, place the Python script in the
same directory as the XML configuration file, or provide a soft link to it.
Ensure the following command line tools are on the system path:

pysam - Python interface to samtools (http://code.google.com/p/pysam/)
genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
bedGraphToBigWig  - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)

Credits
-------

Original script by Brad Chapman, revisions from Peter Cock including the
switch to using genomeCoverageBed and bedGraphToBigWig based on the work
of Lance Parsons.

License
------

The code is freely available under the MIT license:
http://www.opensource.org/licenses/mit-license.html