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+===============
+Bismark Wrapper
+===============
+
+Bismark_ uses Bowtie or Bowtie2 to map bisulfite converted sequence reads to a reference genome and determine cytosine methylation states.
+
+Publication: http://www.ncbi.nlm.nih.gov/pubmed/21493656
+
+User Guide: http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide_v0.7.12.pdf
+
+.. _bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
+
+Preparation
+===========
+
+Create your reference index with *bismark_genome_preparation* in your normal Galaxy Bowtie2/Botwie index directory. It will create a Bisulfite_Genome folder directly in your Bowtie2/Bowtie index directory.
+If you follow that approach you do not need to specify or modify an extra .loc file.
+That wrapper will extract the path to the Bisulfite_Genome folder from ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.
+
+=======
+History
+=======
+
+- v0.7: Initial public release
+- v0.7.8: update and add Tool Shed Integration
+- v0.7.11.1 change default output to BAM, from now on samtools are required
+- v0.7.11.2 added multi-threading to samtools (samtools > 0.1.19 is required)
+- v0.7.12 upgrade to bismark 0.7.12 and fix a major slowdown
+
+===============================
+Wrapper Licence (MIT/BSD style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+