# HG changeset patch
# User brad-chapman
# Date 1307478346 14400
# Node ID d2c1af6570100e913fdcbee067ed1846ebe0d2ec
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
diff -r 000000000000 -r d2c1af657010 bam_to_bigwig/README.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig/README.txt Tue Jun 07 16:25:46 2011 -0400
@@ -0,0 +1,15 @@
+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.
+
+The latest version of the bam_to_wiggle.py script is available at:
+
+https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
+
+This requires:
+
+Python2, version 2.6 or better
+pysam (http://code.google.com/p/pysam/)
+wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
diff -r 000000000000 -r d2c1af657010 bam_to_bigwig/bam_to_bigwig.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig/bam_to_bigwig.xml Tue Jun 07 16:25:46 2011 -0400
@@ -0,0 +1,25 @@
+
+ Calculates coverage from a BAM alignment file
+ bam_to_wiggle.py $align --outfile=$out
+
+
+
+
+
+
+
+
+**What it does**
+
+Creates a coverage file in BigWig format, given a BAM alignment file.
+
+**Input**
+
+A BAM alignment file. This needs to have the genome database build used in alignment annotated. If your file has '?' for the database build, click on the pencil icon to edit the alignment attributes, and specify the organism used to align against.
+
+**Output**
+
+BigWig files can be loaded directly from Galaxy into the UCSC browser. They can be loaded incrementally by UCSC, so a single file can be used to represent the entire genome without having to upload the entire thing as a custom track.
+
+
+
diff -r 000000000000 -r d2c1af657010 bam_to_bigwig/bam_to_wiggle.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_bigwig/bam_to_wiggle.py Tue Jun 07 16:25:46 2011 -0400
@@ -0,0 +1,123 @@
+#!/usr/bin/env python
+"""Convert BAM files to BigWig file format in a specified region.
+
+Usage:
+ bam_to_wiggle.py []
+ [--outfile=