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+++ b/tools/effectiveT3/effectiveT3.txt	Tue Apr 30 09:32:56 2013 -0400
@@ -0,0 +1,125 @@
+Galaxy wrapper for EffectiveT3 v1.0.1
+=====================================
+
+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.
+
+This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
+
+Jehl, Arnold and Rattei.
+Effective - a database of predicted secreted bacterial proteins
+Nucleic Acids Research, 39(Database issue), D591-5, 2011.
+http://dx.doi.org/10.1093/nar/gkq1154
+
+Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
+Sequence-based prediction of type III secreted proteins.
+PLoS Pathog. 5(4):e1000376, 2009.
+http://dx.doi.org/10.1371/journal.ppat.1000376
+
+http://effectors.org/
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
+
+
+Manual Installation
+===================
+
+You can change the path by setting the environment variable EFFECTIVET3 to the
+relevant folder, but by default it expects the following files to be installed
+at these locations:
+
+/opt/EffectiveT3/TTSS_GUI-1.0.1.jar
+/opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
+/opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
+/opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a tools/effectiveT3 folder:
+
+* effectiveT3.xml (the Galaxy tool definition)
+* effectiveT3.py (the Python wrapper script)
+* effectiveT3.txt (this README file)
+
+Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
+(and edit if appropriate, e.g. to add or remove a model).
+
+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="effectiveT3/effectiveT3.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 effectiveT3
+
+That's it.
+
+
+History
+=======
+
+v0.0.7 - Initial public release
+v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
+v0.0.9 - Check the return code for errors in the XML
+v0.0.10- Added unit test
+v0.0.11- Automated installation
+       - Record version of Python script when called from Galaxy
+
+
+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 effectiveT3.tar.gz tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.txt tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
+
+
+Check this worked:
+
+$ tar -tzf effectiveT3.tar.gz
+tools/effectiveT3/effectiveT3.xml
+tools/effectiveT3/effectiveT3.py
+tools/effectiveT3/effectiveT3.txt
+tools/effectiveT3/tool_dependencies.xml
+tool-data/effectiveT3.loc.sample
+test-data/four_human_proteins.fasta
+test-data/four_human_proteins.effectiveT3.tabular
+test-data/empty.fasta
+test-data/empty_effectiveT3.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.
+EffectiveT3 is available and licenced separately.