Mercurial > repos > mikel-egana-aranguren > ncbo_services
changeset 0:e25b2c00fffd
first version
| author | mikel-egana-aranguren |
|---|---|
| date | Sat, 31 Dec 2011 10:08:28 -0500 |
| parents | |
| children | d0cff9cccc25 |
| files | NCBO_services/README NCBO_services/get_ontology.jar NCBO_services/get_ontology.xml NCBO_services/get_ontology_lib/commons-codec-1.4.jar NCBO_services/get_ontology_lib/commons-logging-1.1.1.jar NCBO_services/get_ontology_lib/httpclient-4.1.2.jar NCBO_services/get_ontology_lib/httpclient-cache-4.1.2.jar NCBO_services/get_ontology_lib/httpcore-4.1.2.jar NCBO_services/get_ontology_lib/httpmime-4.1.2.jar |
| diffstat | 9 files changed, 110 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/README Sat Dec 31 10:08:28 2011 -0500 @@ -0,0 +1,81 @@ + + + + ============= + NCBO Services + ============= + + + +INSTALLATION +============ + +1.- Stop Galaxy. + +2.- Copy the .jar files and _lib/ directories to +/galaxy-dist/tool-data/shared/jars/ + +3.- Create directory /galaxy-dist/tools/NCBO_services/ + +4.- Copy get_ontology.xml to /galaxy-dist/tools/NCBO_services/ + +5.- Add the following lines to /galaxy-dist/tool_conf.xml: + + <section name="NCBO services" id="NCBO_services"> + <tool file="NCBO_services/get_ontology.xml"/> + </section> + +6.- Start Galaxy. + + + +USAGE +===== + +A bioportal API key and an ontology id must be provided. The API key can be +obtained by creating an account at bioportal +(http://bioportal.bioontology.org/). The id can be obtained in the ontology page +(e.g. 1522 for BioPAX, see http://bioportal.bioontology.org/ontologies/1522) + + + +CONTACT +======= + +Please send any request or comment to mikel.egana.aranguren@gmail.com. + + + +ACKNOWLEDGEMENTS +================ + +This work is funded by the Marie Curie Cofund program of the EU, FP7. + + + +COPYRIGHT AND LICENSE +===================== + +Copyright (c) 2011 Mikel Egaña Aranguren. + +NCBO Services is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see <http://www.gnu.org/licenses/>. + + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/get_ontology.xml Sat Dec 31 10:08:28 2011 -0500 @@ -0,0 +1,29 @@ +<tool id="get_ontology" name="Get ontology by id" version="1.0.0"> + <description>Retrieves an ontology from bioportal using its id</description> + <command>java -jar ${__tool_data_path__}/shared/jars/ncbo_galaxy.jar $api_key $ontology_id > $output </command> + <inputs> + <param name="api_key" type="text" size="100" label="BioPortal API key" /> + <param name="ontology_id" type="text" size="100" label="Ontology ID from bioportal" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="api_key" value="74c12fc6-9423-455a-a619-b94f47d1951b"/> + <param name="ontology_id" value="1522"/> + </test> + </tests> + <help> + +**Usage** + + Enter bioportal API key and ontology id (e.g. 1522 for BioPAX), and the ontology will be retrieved. + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + </help> + +</tool>