Mercurial > repos > peterjc > effectivet3
changeset 4:f7ce32e13bc6 draft
Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
| author | peterjc |
|---|---|
| date | Wed, 18 Sep 2013 06:11:36 -0400 |
| parents | b0b927299aee |
| children | 1ea715da1879 |
| files | tools/effectiveT3/README.rst tools/effectiveT3/effectiveT3.txt tools/effectiveT3/effectiveT3.xml |
| diffstat | 3 files changed, 156 insertions(+), 136 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ 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.
--- a/tools/effectiveT3/effectiveT3.txt Thu May 16 04:45:41 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,129 +0,0 @@ -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) -* 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 - - Link to Tool Shed added to help text and this documentation. - - -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.
--- a/tools/effectiveT3/effectiveT3.xml Thu May 16 04:45:41 2013 -0400 +++ b/tools/effectiveT3/effectiveT3.xml Wed Sep 18 06:11:36 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="effectiveT3" name="Effective T3" version="0.0.11"> +<tool id="effectiveT3" name="Effective T3" version="0.0.12"> <description>Find bacterial effectors in protein sequences</description> <requirements> <requirement type="package" version="1.0.1">effectiveT3</requirement> @@ -40,7 +40,7 @@ </conditional> </inputs> <outputs> - <data name="tabular_file" format="tabular" label="$module.value_label results" /> + <data name="tabular_file" format="tabular" label="Effective T3 $module.value_label on ${on_string}" /> </outputs> <tests> <test> @@ -76,17 +76,25 @@ **References** -Jehl, Arnold and Rattei. +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 + +Jehl, Arnold and Rattei (2011). Effective - a database of predicted secreted bacterial proteins -Nucleic Acids Research, 39(Database issue), D591-5, 2011. +Nucleic Acids Research, 39(Database issue), D591-5. http://dx.doi.org/10.1093/nar/gkq1154 -Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei. +Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009). Sequence-based prediction of type III secreted proteins. -PLoS Pathog. 5(4):e1000376, 2009. +PLoS Pathog. 5(4):e1000376. http://dx.doi.org/10.1371/journal.ppat.1000376 -http://effectors.org/ +See also http://effectors.org/ This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3