# HG changeset patch
# User Lance Parsons <lparsons@princeton.edu>
# Date 1337966406 14400
# Node ID 73e1e4d0b419294411a14551d1ebf438afd74440
# Parent  c1f3ee7b5003ed1c74546e79e028f559cff15fdf
Deprecated this version

diff -r c1f3ee7b5003 -r 73e1e4d0b419 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri May 25 13:20:06 2012 -0400
@@ -0,0 +1,12 @@
+This tool was based on an early version of the Freebayes Galaxy wrapper that was included with Galaxy.  Since then, the included tool written by Daniel Blankenberg has been updated and is generally preferred since it works with newer versions of Freebayes and supports more options.
+
+This tool uses Freebayes to call SNPS given a reference sequence and a BAM alignment file.
+http://bioinformatics.bc.edu/marthlab/FreeBayes
+
+Base alignment quality (BAQ) adjustment is a quality smoothing filter which applies a hidden 
+markov model of read genesis to each alignment independently.  This is currently implemented
+by samtools fillmd.  (See Biological Sequence Analysis Probabilistic Models of Proteins and 
+Nucleic Acids by Durbin et. al. for more details.)
+
+
+Updated in 2011 by Lance Parsons <lparsons@princeton.edu>, Lewis-Sigler Institute for Integrative Genomics, Princeton University
diff -r c1f3ee7b5003 -r 73e1e4d0b419 freebayes.xml
--- a/freebayes.xml	Fri May 25 13:09:44 2012 -0400
+++ b/freebayes.xml	Fri May 25 13:20:06 2012 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="freebayes_wrapper_princeton" name="Call SNPS with Freebayes (beta)" version="0.9.0.a">
+<tool id="freebayes_wrapper_princeton" name="Call SNPS with Freebayes (DEPRECATED)" version="0.9.0.a">
   <requirements>
     <requirement type="package" version="0.9.0">freebayes</requirement>
     <requirement type="package">samtools</requirement>