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+++ b/tools/effectiveT3/README.rst	Wed Sep 18 06:11:36 2013 -0400
@@ -0,0 +1,141 @@
+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/
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
+
+
+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)
+* README.rst (this 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. Then::
+
+    $ ./run_functional_tests.sh -id effectiveT3
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+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
+        - Link to Tool Shed added to help text and this documentation.
+v0.0.12 - More explicit naming of the output dataset.
+        - Adopt 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/effectiveT3
+
+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/README.rst tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py 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/README.rst
+    tools/effectiveT3/effectiveT3.xml
+    tools/effectiveT3/effectiveT3.py
+    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)
+=============
+
+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.
+EffectiveT3 is available and licenced separately.