# HG changeset patch
# User fubar
# Date 1380365324 14400
# Node ID 5022cd74093c384d34e00762d7b1ec68a3e7c5da
# Parent  9a7e8a919c78dfdedd7384b1a6cf90cbfcd3f034
Uploaded

diff -r 9a7e8a919c78 -r 5022cd74093c freebayes-d291dc763c4c/freebayes.xml
--- a/freebayes-d291dc763c4c/freebayes.xml	Sat Sep 28 05:57:27 2013 -0400
+++ b/freebayes-d291dc763c4c/freebayes.xml	Sat Sep 28 06:48:44 2013 -0400
@@ -433,6 +433,7 @@
     </test>
   </tests>
   <help>
+      
 **What it does**
 
 This tool uses FreeBayes 0.9.9 to call SNPS given a reference sequence and a BAM alignment file.
@@ -441,9 +442,10 @@
 
 In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. 
 
-Go `here &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_ for details on FreeBayes.
+Go FreeBayesMarth_ for details on FreeBayes.
 
-or `here &lt;https://github.com/ekg/freebayes&gt;`_ 
+or FreeBayesGit_ for source
+
 ------
 
 **Inputs**
@@ -670,11 +672,17 @@
 
 ------
 
+
 **Citation**
 
 For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing &lt;http://arxiv.org/abs/1207.3907&gt;`_.
 
 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
 
+.. _FreeBayesMarth: http://bioinformatics.bc.edu/marthlab/FreeBayes
+
+.. _FreeBayesGit: https://github.com/ekg/freebayes
+
+.. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html
   </help>
 </tool>