diff README.txt @ 7:77114c36b8ab draft default tip

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Mon Aug 29 07:28:10 2016 -0400
@@ -0,0 +1,48 @@
+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