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