Mercurial > repos > brad-chapman > bam_to_bigwig

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/bam_to_bigwig/ commit b5c3df21127fc27f66a97761173c07e161f2fa8e
author lparsons
date Thu, 12 May 2016 11:39:13 -0400
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5:52bcd04ee0d6 6:9163e1db4c16
1 Convert a BAM file into a BigWig coverage file. This can be used directly from
2 Galaxy for display at UCSC. The advantage over standard Wiggle format is that
3 the data is stored in a compressed format and can be retrieved by genome
4 region. This allows you to view regions of arbitrarily large Wiggle file data
5 at UCSC while avoiding the upload costs.
6
7 History
8 -------
9
10 v0.2.0 add a sort step after genomeCoverageBed which is required in some
11 instances otherwise bedGraphToBigWig will complain. This version also uses
12 Galaxy's dependency mechanism, added some tests, and updated some formatting.
13 By Lance Parsons.
14
15 v0.1.1 passes the forgotten split argument and moves to using the new
16 sub-command enabled bedtools. Thanks to David Leader.
17
18 As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using
19 genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to
20 be excluded from the coverage calculation, which is important for RNA-Seq.
21
22 Until v0.0.2, this Galaxy tool used the bam_to_wiggle.py script from
23 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
24 which internally used pysam (and thus samtools) and wigToBigWig from UCSC.
25
26 Requirements
27 ------------
28
29 If you are installing this tool manually, place the Python script in the
30 same directory as the XML configuration file, or provide a soft link to it.
31 Ensure the following command line tools are on the system path:
32
33 pysam - Python interface to samtools (http://code.google.com/p/pysam/)
34 genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
35 bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
36
37 Credits
38 -------
39
40 Original script by Brad Chapman, revisions from Peter Cock including the
41 switch to using genomeCoverageBed and bedGraphToBigWig based on the work
42 of Lance Parsons.
43
44 License
45 ------
46
47 The code is freely available under the MIT license:
48 http://www.opensource.org/licenses/mit-license.html