annotate get_ontology_view.xml @ 27:e2b16720ef25 draft

Directories re-arranged for easier installation via mercurial
author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Mon, 08 Oct 2012 14:25:04 +0200
parents NCBO_services/get_ontology_view.xml@4cd75b0d77af
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
1 <tool id="get_ontology_view" name="Get a concrete view of an ontology" version="1.0.1">
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
2 <description>Retrieves a view of an ontology using the view id</description>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
3 <command>java -jar ${__tool_data_path__}/shared/jars/get_ontology_view.jar $api_key $ontologyviewid > $output </command>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
4
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
5 <inputs>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
6 <param name="api_key" type="text" size="100" label="BioPortal API key" />
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
7 <param name="ontologyviewid" type="text" size="100" label="Ontology view ID" />
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
8 </inputs>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
9 <outputs>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
10 <data format="text" name="output" />
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
11 </outputs>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
12 <tests>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
13 <test>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
14 <param name="api_key"/>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
15 </test>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
16 </tests>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
17 <help>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
18
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
19 **What it does**
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
20
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
21 It retrieves a view from an ontology contained in BioPortal.
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
22
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
23 **Parameters**
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
24
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
25 * Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org.
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
26 * Ontology view ID: it can be obtained from BioPortal, in the Ontology page, on the views section, by looking at the view URL. For example, it is 41014 for the generic Gene Ontology slim.
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
27
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
28 **Contact**
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
29
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
30 Please send any request or comment to mikel.egana.aranguren@gmail.com.
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
31
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
32 **More information**
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
33
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
34 http://bioportal.bioontology.org
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
35
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
36 http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
37
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
38 </help>
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
39
4cd75b0d77af get ontology view tool added
Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
parents:
diff changeset
40 </tool>