--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/nlstradamus/README.rst	Wed Sep 18 06:15:33 2013 -0400
@@ -0,0 +1,128 @@
+Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
+=========================================================
+
+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 (MIT licence).
+
+NLStradamus is a command line tool for predicting nuclear localization
+signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
+
+A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
+NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
+BMC Bioinformatics. 2009 Jun 29;10(1):202.
+http://dx.doi.org/10.1186/1471-2105-10-202
+
+http://www.moseslab.csb.utoronto.ca/NLStradamus
+
+Early versions of NLStradamus did not have a native tabular output format, this
+was added in version 1.7. Additionally a fast C++ implementation was added at
+this point (early versions of NLStradamus came as a perl script only).
+
+Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
+unchanged.
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the C++ implementation of NLStradamus v1.8, and run the unit tests.
+
+
+Manual Installation
+===================
+This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
+PATH.
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a tools/protein_analysis folder:
+
+* nlstradamus.xml (the Galaxy tool definition)
+* nlstradamus.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 (matching the chosen install path)::
+
+  <tool file="protein_analysis/nlstradamus.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 nlstradamus
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.3  - Initial public release
+v0.0.4  - Adding DOI link to reference
+          (Documentation change only)
+v0.0.5  - Assume non-zero return codes are errors
+v0.0.6  - Show output help text using a table
+        - Added unit tests
+v0.0.7  - Automatic installation of the NLStradamus binary when installed
+          via the Galaxy Tool Shed
+v0.0.8  - Link to Tool Shed added to help text and this documentation.
+        - Use reStructuredText for this README file.
+        - Adopted standard MIT licence.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools are being 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/nlstradamus
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf nlstradmus.tar.gz tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
+
+Check this worked::
+
+    $ tar -tzf nlstradmus.tar.gz
+    tools/nlstradamus/README.rst
+    tools/nlstradamus/nlstradamus.xml
+    tools/nlstradamus/tool_dependencies.xml
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.nlstradamus.tabular
+    test-data/empty.fasta
+    test-data/empty_nlstradamus.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.

--- a/tools/nlstradamus/nlstradamus.txt	Tue Apr 23 11:59:14 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
-=========================================================
-
-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.
-
-NLStradamus is a command line tools for predicting nuclear localization
-signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).
-
-A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
-NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
-BMC Bioinformatics. 2009 Jun 29;10(1):202.
-http://dx.doi.org/10.1186/1471-2105-10-202
-
-http://www.moseslab.csb.utoronto.ca/NLStradamus
-
-Early versions of NLStradamus did not have a native tabular output format, this
-was added in version 1.7. Additionally a fast C++ implementation was added at
-this point (early versions of NLStradamus came as a perl script only).
-
-Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
-unchanged.
-
-
-Automated Installation
-======================
-
-This should be straightforward, Galaxy should automatically download and install
-the C++ implementation of NLStradamus v1.8, and run the unit tests.
-
-
-Manual Installation
-===================
-This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
-PATH.
-
-To install the wrapper copy or move the following files under the Galaxy tools
-folder, e.g. in a tools/protein_analysis folder:
-
-* nlstradamus.xml (the Galaxy tool definition)
-* nlstradamus.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 (matching the chosen install path):
-
-<tool file="protein_analysis/nlstradamus.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 nlstradamus
-
-That's it.
-
-
-History
-=======
-
-v0.0.3 - Initial public release
-v0.0.4 - Adding DOI link to reference
-         (Documentation change only)
-v0.0.5 - Assume non-zero return codes are errors
-v0.0.6 - Show output help text using a table
-       - Added unit tests
-v0.0.7 - Automatic installation of the NLStradamus binary when installed
-         via the Galaxy Tool Shed
-
-
-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 nlstradmus.tar.gz tools/nlstradamus/nlstradamus.xml tools/nlstradamus/nlstradamus.txt tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
-
-Check this worked:
-
-$ tar -tzf nlstradmus.tar.gz
-tools/nlstradamus/nlstradamus.xml
-tools/nlstradamus/nlstradamus.txt
-tools/nlstradamus/tool_dependencies.xml
-test-data/four_human_proteins.fasta
-test-data/four_human_proteins.nlstradamus.tabular
-test-data/empty.fasta
-test-data/empty_nlstradamus.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. NLStradamus
-is is available and licenced separately (under the GPL v3 or later).

--- a/tools/nlstradamus/nlstradamus.xml	Tue Apr 23 11:59:14 2013 -0400
+++ b/tools/nlstradamus/nlstradamus.xml	Wed Sep 18 06:15:33 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="nlstradamus" name="NLStradamus" version="0.0.7">
+<tool id="nlstradamus" name="NLStradamus" version="0.0.8">
     <description>Find nuclear localization signals (NLSs) in protein sequences</description>
     <command>
       NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
@@ -71,12 +71,23 @@
 
 **References**
 
-A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
+
+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
+
+A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses (2009).
 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
-BMC Bioinformatics. 2009 Jun 29;10(1):202.
+BMC Bioinformatics 10(1):202.
 http://dx.doi.org/10.1186/1471-2105-10-202
 
-http://www.moseslab.csb.utoronto.ca/NLStradamus
+See also http://www.moseslab.csb.utoronto.ca/NLStradamus
 
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
     </help>
 </tool>