# HG changeset patch
# User mikel-egana-aranguren
# Date 1325344108 18000
# Node ID e25b2c00fffddf1da668b640d18dad9bec61ccd5

first version

diff -r 000000000000 -r e25b2c00fffd NCBO_services/README
--- /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/>.
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r e25b2c00fffd NCBO_services/get_ontology.jar
Binary file NCBO_services/get_ontology.jar has changed
diff -r 000000000000 -r e25b2c00fffd NCBO_services/get_ontology.xml
--- /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>
diff -r 000000000000 -r e25b2c00fffd NCBO_services/get_ontology_lib/commons-codec-1.4.jar
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diff -r 000000000000 -r e25b2c00fffd NCBO_services/get_ontology_lib/commons-logging-1.1.1.jar
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diff -r 000000000000 -r e25b2c00fffd NCBO_services/get_ontology_lib/httpclient-4.1.2.jar
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diff -r 000000000000 -r e25b2c00fffd NCBO_services/get_ontology_lib/httpcore-4.1.2.jar
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diff -r 000000000000 -r e25b2c00fffd NCBO_services/get_ontology_lib/httpmime-4.1.2.jar
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