diff readme.rst @ 0:d4a2c739da3f draft

Initial release under a consistent username. Fixes for stdout and the trailing semicolon.

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+===============================
+Galaxy wrapper for RepeatMasker
+===============================
+
+This wrapper is copyright 2013 by Björn Grüning.
+
+This is a wrapper for the command line tool of RepeatMasker from the Institute for Systems Biology.
+http://www.repeatmasker.org/
+
+
+Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0.
[phone] <http://www.repeatmasker.org>. 
+
+
+Additional Information:
+Using RepeatMasker to identify repetitive elements in genomic sequences.
+http://www.ncbi.nlm.nih.gov/pubmed/19274634
+
+============
+Installation
+============
+
+To install RepeatMasker, please use the following instructions:
+
+http://www.repeatmasker.org/RMDownload.html
+
+To install the wrapper copy the file RepeatMasker.xml in the galaxy tools
+folder and modify the tools_conf.xml file to make the tool available to Galaxy.
+Add a line like the following:
+
+Add the tool definition to your tool_conf.xml file under Galaxy root.
+	<tool file="RepeatMasker/RepeatMasker.xml" />
+
+=======
+History
+=======
+
+- v1.1: Initial public release
+- v0.1.1: patch from Simon Guest, to create empty files if no repeat is found
+- v0.1.2: remove trailing semicolon, redirect all output to stdout
+
+===============================
+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.
+