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Commit message:
Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub |
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modified:
tools/clinod/clinod.xml |
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added:
tools/clinod/README.rst |
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removed:
tools/clinod/clinod.txt |
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| diff -r d1aebb0acee7 -r 6a9debe4b860 tools/clinod/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/clinod/README.rst Wed Sep 18 06:09:33 2013 -0400 |
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| @@ -0,0 +1,119 @@ +Galaxy wrapper for Command line NoD predictor (v1.3) +==================================================== + +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. + +Command line NoD predictor is a tool for predicting nucleolar localization +sequences (NoLSs) in a FASTA file of proteins using a neural network. There +is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/ + +This NoD wrapper is available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/peterjc/clinod + + +Automated Installation +====================== + +This should be straightforward, Galaxy should automatically download and install +the JAR file for clinod v1.3 and the batchman executable from the Stuttgart +Neural Network Simulator (SNNS), and set the $CLINOD to their folder. + + +Manual Installation +=================== +This wrapper expects the java binary to be on the system PATH, and to be able +to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used +/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod + +Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network +Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the +system path or located next to the JAR file, i.e. /opt/clinod/batchman + +To install the wrapper copy or move the following files under the Galaxy tools +folder, e.g. in a tools/clinod folder: + +* clinod.xml (the Galaxy tool definition) +* README.rst (this 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:: + + <tool file="clinod/clinod.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 clinod + +That's it. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial public release +v0.0.2 - Treat non-zero return codes as errors +v0.0.3 - Describe output table in help +v0.0.4 - Added unit test +v0.0.5 - Link to Tool Shed added to help text and this documentation. + - Automated tool installation. +v0.0.6 - Adopted 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/clinod + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder:: + + $ tar -czf clinod.tar.gz tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular + +Check this worked:: + + $ tar -tzf clinod.tar.gz + tools/clinod/README.rst + tools/clinod/clinod.xml + tools/clinod/tool_dependencies.xml + test-data/four_human_proteins.fasta + test-data/four_human_proteins.clinod-1.3.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. Command line +NoD is available and licenced separately. |
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| diff -r d1aebb0acee7 -r 6a9debe4b860 tools/clinod/clinod.txt --- a/tools/clinod/clinod.txt Thu May 30 13:26:33 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,108 +0,0 @@ -Galaxy wrapper for Command line NoD predictor (v1.3) -==================================================== - -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. - -Command line NoD predictor is a tool for predicting nucleolar localization -sequences (NoLSs) in a FASTA file of proteins using a neural network. There -is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/ - -This NoD wrapper is available from the Galaxy Tool Shed at: -http://toolshed.g2.bx.psu.edu/view/peterjc/clinod - - -Automated Installation -====================== - -This should be straightforward, Galaxy should automatically download and install -the JAR file for clinod v1.3 and the batchman executable from the Stuttgart -Neural Network Simulator (SNNS), and set the $CLINOD to their folder. - - -Manual Installation -=================== -This wrapper expects the java binary to be on the system PATH, and to be able -to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used -/opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod - -Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network -Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the -system path or located next to the JAR file, i.e. /opt/clinod/batchman - -To install the wrapper copy or move the following files under the Galaxy tools -folder, e.g. in a tools/clinod folder: - -* clinod.xml (the Galaxy tool definition) -* clinod.txt (this README file) - -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the -tool. If you are using other protein analysis tools like TMHMM or SignalP, put -it next to them. Just add the line: - -<tool file="clinod/clinod.xml" /> - -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. - -$ ./run_functional_tests.sh -id clinod - -That's it. - - -History -======= - -v0.0.1 - Initial public release -v0.0.2 - Treat non-zero return codes as errors -v0.0.3 - Describe output table in help -v0.0.4 - Added unit test -v0.0.5 - Link to Tool Shed added to help text and this documentation. - - Automated tool installation. - - -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 clinod.tar.gz tools/clinod/clinod.xml tools/clinod/clinod.txt tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular - -Check this worked: - -$ tar -tzf clinod.tar.gz -tools/clinod/clinod.xml -tools/clinod/clinod.txt -tools/clinod/tool_dependencies.xml -test-data/four_human_proteins.fasta -test-data/four_human_proteins.clinod-1.3.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. Command line -NoD is available and licenced separately. |
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| diff -r d1aebb0acee7 -r 6a9debe4b860 tools/clinod/clinod.xml --- a/tools/clinod/clinod.xml Thu May 30 13:26:33 2013 -0400 +++ b/tools/clinod/clinod.xml Wed Sep 18 06:09:33 2013 -0400 |
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| @@ -58,17 +58,25 @@ **References** -M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton. +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 + +M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton (2010). Characterization and prediction of protein nucleolar localization sequences. -Nucleic Acids Research 38(21), 7388-7399, 2010. +Nucleic Acids Research 38(21), 7388-7399. http://dx.doi.org/10.1093/nar/gkq653 -M. S. Scott, P. V. Troshin and G. J. Barton. +M. S. Scott, P. V. Troshin and G. J. Barton (2011). NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. -BMC Bioinformatics, 12:317, 2011. +BMC Bioinformatics, 12:317. http://dx.doi.org/10.1186/1471-2105-12-317 -http://www.compbio.dundee.ac.uk/www-nod/ +See also http://www.compbio.dundee.ac.uk/www-nod/ This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod |