--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/clinod/README.rst	Wed Sep 18 06:09:33 2013 -0400
@@ -0,0 +1,119 @@
+Galaxy wrapper for Command line NoD predictor (v1.3)
+====================================================
+
+This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+Command line NoD predictor is a tool for predicting nucleolar localization
+sequences (NoLSs) in a FASTA file of proteins using a neural network. There
+is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/
+
+This NoD wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the JAR file for clinod v1.3 and the batchman executable from the Stuttgart
+Neural Network Simulator (SNNS), and set the $CLINOD to their folder.
+
+
+Manual Installation
+===================
+This wrapper expects the java binary to be on the system PATH, and to be able
+to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used
+/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod
+
+Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
+Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
+system path or located next to the JAR file, i.e. /opt/clinod/batchman
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a tools/clinod folder:
+
+* clinod.xml (the Galaxy tool definition)
+* README.rst (this file)
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. If you are using other protein analysis tools like TMHMM or SignalP, put
+it next to them. Just add the line::
+
+  <tool file="clinod/clinod.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder. Then::
+
+    $ ./run_functional_tests.sh -id clinod
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial public release
+v0.0.2  - Treat non-zero return codes as errors
+v0.0.3  - Describe output table in help
+v0.0.4  - Added unit test
+v0.0.5  - Link to Tool Shed added to help text and this documentation.
+        - Automated tool installation.
+v0.0.6  - Adopted standard MIT licence.
+        - Use reStructuredText for this README file.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf clinod.tar.gz tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular
+
+Check this worked::
+
+    $ tar -tzf clinod.tar.gz
+    tools/clinod/README.rst
+    tools/clinod/clinod.xml
+    tools/clinod/tool_dependencies.xml
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.clinod-1.3.tabular
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+NOTE: This is the licence for the Galaxy Wrapper only. Command line
+NoD is available and licenced separately.

--- a/tools/clinod/clinod.txt	Thu May 30 13:26:33 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,108 +0,0 @@
-Galaxy wrapper for Command line NoD predictor (v1.3)
-====================================================
-
-This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-Command line NoD predictor is a tool for predicting nucleolar localization
-sequences (NoLSs) in a FASTA file of proteins using a neural network. There
-is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/
-
-This NoD wrapper is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
-
-
-Automated Installation
-======================
-
-This should be straightforward, Galaxy should automatically download and install
-the JAR file for clinod v1.3 and the batchman executable from the Stuttgart
-Neural Network Simulator (SNNS), and set the $CLINOD to their folder.
-
-
-Manual Installation
-===================
-This wrapper expects the java binary to be on the system PATH, and to be able
-to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used
-/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod
-
-Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
-Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
-system path or located next to the JAR file, i.e. /opt/clinod/batchman
-
-To install the wrapper copy or move the following files under the Galaxy tools
-folder, e.g. in a tools/clinod folder:
-
-* clinod.xml (the Galaxy tool definition)
-* clinod.txt (this README file)
-
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
-tool. If you are using other protein analysis tools like TMHMM or SignalP, put
-it next to them. Just add the line:
-
-<tool file="clinod/clinod.xml" />
-
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder.
-
-$ ./run_functional_tests.sh -id clinod
-
-That's it.
-
-
-History
-=======
-
-v0.0.1 - Initial public release
-v0.0.2 - Treat non-zero return codes as errors
-v0.0.3 - Describe output table in help
-v0.0.4 - Added unit test
-v0.0.5 - Link to Tool Shed added to help text and this documentation.
-       - Automated tool installation.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-$ tar -czf clinod.tar.gz tools/clinod/clinod.xml tools/clinod/clinod.txt tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular
-
-Check this worked:
-
-$ tar -tzf clinod.tar.gz
-tools/clinod/clinod.xml
-tools/clinod/clinod.txt
-tools/clinod/tool_dependencies.xml
-test-data/four_human_proteins.fasta
-test-data/four_human_proteins.clinod-1.3.tabular
-
-
-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.
-
-NOTE: This is the licence for the Galaxy Wrapper only. Command line
-NoD is available and licenced separately.

--- a/tools/clinod/clinod.xml	Thu May 30 13:26:33 2013 -0400
+++ b/tools/clinod/clinod.xml	Wed Sep 18 06:09:33 2013 -0400
@@ -58,17 +58,25 @@
 
 **References**
 
-M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton (2010).
 Characterization and prediction of protein nucleolar localization sequences.
-Nucleic Acids Research 38(21), 7388-7399, 2010.
+Nucleic Acids Research 38(21), 7388-7399.
 http://dx.doi.org/10.1093/nar/gkq653
 
-M. S. Scott, P. V. Troshin and G. J. Barton.
+M. S. Scott, P. V. Troshin and G. J. Barton (2011).
 NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins.
-BMC Bioinformatics, 12:317, 2011.
+BMC Bioinformatics, 12:317.
 http://dx.doi.org/10.1186/1471-2105-12-317
 
-http://www.compbio.dundee.ac.uk/www-nod/
+See also http://www.compbio.dundee.ac.uk/www-nod/
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod