| Next changeset 1:221d7dca03a5 (2013-04-16) |
|
Commit message:
Uploaded wrapper v0.0.1 (for clinod v1.3) |
|
added:
tools/protein_analysis/clinod.txt tools/protein_analysis/clinod.xml |
| b |
| diff -r 000000000000 -r b8be455c27d1 tools/protein_analysis/clinod.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/clinod.txt Tue Aug 02 06:51:52 2011 -0400 |
| b |
| @@ -0,0 +1,84 @@ +Galaxy wrapper for Command line NoD predictor (v1.3) +==================================================== + +This wrapper is copyright 2011 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/ + + +Installation +============ +This wrapper expects the java binary to be on the system PATH, and to be able +to access command line NoD as /opt/clinod/clinod-1.3.jar (edit clinod.xml if +you wish to use a different location). + +Internally NoD calls the binary batchman from the Stuttgart Neural Network +Simulator (SNNS) v 4.2 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/protein_analysis 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="protein_analysis/clinod.xml" /> + +That's it. + + +History +======= + +v0.0.1 - Initial public release + + +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://community.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder: + +$ tar -czf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt + +Check this worked: + +$ tar -tzf clinod.tar.gz +tools/protein_analysis/clinod.xml +tools/protein_analysis/clinod.txt + + +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. |
| b |
| diff -r 000000000000 -r b8be455c27d1 tools/protein_analysis/clinod.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/clinod.xml Tue Aug 02 06:51:52 2011 -0400 |
| b |
| @@ -0,0 +1,53 @@ +<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.1"> + <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> + <command> + java -jar /opt/clinod/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=8 -f=MEDIUM_TAB -nonols -clean_sequence + ##I want the number of threads to be a Galaxy config option... + ##TODO - Make the -clean_sequece argument a parameter? + </command> + <inputs> + <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> + </inputs> + <outputs> + <data name="tabular_file" format="tabular" label="NoD results" /> + </outputs> + <requirements> + <requirement type="binary">java</requirement> + </requirements> + <help> + +**What it does** + +This calls the command line version of the NoD tool from the Barton Group for +prediction of nucleolar localization sequences (NoLSs). The NoD tool uses an +artificial neural network trained on a set of human NoLSs. + +The nucleolus is a sub-compartmentof the nucleus, thus an NoLS can be regarded +as a special nuclear localization sequence (NLS). + +The input is a FASTA file of protein sequences, and the output is tabular with +four columns (multiple rows per protein): + + * Sequence identifier + * Start of NoLS + * End of NoLS + * NoLS sequence + +If a sequence has no predicted NoLS, then there is no line in the output file +for it. + +**References** + +M. S. Scott, F. M. Boisvert, M. D. McDowall, A. I. Lamond and G. J. Barton. +Characterization and prediction of protein nucleolar localization sequences. +Nucleic Acids Research 38(21), 7388-7399, 2010. +http://dx.doi.org/10.1093/nar/gkq653 + +M. S. Scott, P. V. Troshin and G. J. Barton. +NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. +BMC Bioinformatics, in press, 2011. + +http://www.compbio.dundee.ac.uk/www-nod/ + + </help> +</tool> |