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Repository 'effectivet3'
http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
effectivet3
unrestricted
Find bacterial type III effectors in protein sequences
Wrapper for the command line Java tool EffectiveT3, v1.0.1, which converts the output into a tab separated table for use in Galaxy.

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

See http://effectors.org/
4:f7ce32e13bc6
peterjc
True
253

Repository README files - may contain important installation or license information

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.

Dependencies of this repository

Name Version Type
effectiveT3 1.0.1 package

Contents of this repository

Name Description Version
Effective T3 Find bacterial effectors in protein sequences 0.0.12

Automated tool test results

Time tested: 2014-04-17 05:46:40
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
TypeNameVersion
effectiveT3 package 1.0.1
Installation directory
/ToolDepsMain/effectiveT3/1.0.1/peterjc/effectivet3/f7ce32e13bc6
Time tested: 2014-04-16 05:41:02
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
TypeNameVersion
effectiveT3 package 1.0.1
Installation directory
/ToolDepsMain/effectiveT3/1.0.1/peterjc/effectivet3/f7ce32e13bc6
Time tested: 2014-04-15 06:15:38
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
TypeNameVersion
effectiveT3 package 1.0.1
Installation directory
/ToolDepsMain/effectiveT3/1.0.1/peterjc/effectivet3/f7ce32e13bc6
Time tested: 2014-04-14 05:38:04
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13041:b423b847f58e
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
Tool id: effectiveT3
Tool version: effectiveT3
Test: test_tool_000001 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/effectivet3/effectiveT3/0.0.12)
TypeNameVersion
effectiveT3 package 1.0.1
Installation directory
/ToolDepsMain/effectiveT3/1.0.1/peterjc/effectivet3/f7ce32e13bc6

Categories
Sequence Analysis