# HG changeset patch # User saml # Date 1353520530 18000 # Node ID eee537fd46001eeb4557bdf649d6ea78ca3e0a11 # Parent ee072a7d271bdee481cae58cd466cfb6302fcfe6 Uploaded diff -r ee072a7d271b -r eee537fd4600 galaxy_semwebtools --- a/galaxy_semwebtools Wed Nov 21 12:53:24 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,797 +0,0 @@ - - - - - - - saml / galaxy_semwebtools — Bitbucket - - - - - - - - - - - - - - - - - - -

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galaxy_semwebtools

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Semantic Web Tools for Galaxy

SPARQL Import tool

This Galaxy (bioinformatics web portal) toolkit currently just contains a tool that enables to specify an URL to a SPARQL endpoint, and a SPARQL query, and to save the returned data in tabular format, for further processing in Galaxy's tools.

Installation

Create a folder "semweb_tools" under [galaxy_root]/tools/ and add these files.
Add the following section right under the starting <toolbox> tag in [galaxy_root]/tool_conf.xml:

    <section name="Semantic Web Tools" id="semweb_tools">
-        <tool file="semweb_tools/sparql_import.xml" />
-    </section>
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Change log

2012-11-16: Now works properly (at least for my simple test case)!
2012-11-16: Created today, still under heavy development!

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- - - Samuel Lampa - - created - - -saml/galaxy_semwebtools - -

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Owner: Samuel Lampa
Access Level: Public
Type: Mercurial
Language: Python
Last Updated: a minute ago
Created: 4 minutes ago
Size: - 3.9 KB - (download) -

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- - - - - - - - - - - - - - - - - - - diff -r ee072a7d271b -r eee537fd4600 sparql_import.xml --- a/sparql_import.xml Wed Nov 21 12:53:24 2012 -0500 +++ b/sparql_import.xml Wed Nov 21 12:55:30 2012 -0500 @@ -29,16 +29,17 @@ This will generate a 3-column tabular output like this:: - http://identifiers.org/pubmed/12860264 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/15782111 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/11017945 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/10997684 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/19635799 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/16480962 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/15976321 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/17218259 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/17215298 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference - http://identifiers.org/pubmed/11177571 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://vocabularies.wikipathways.org/wp#PublicationReference + + + + + + + + + + +