Mercurial > repos > saml > semweb_tools
changeset 5:eee537fd4600 draft default tip
Uploaded
| author | saml |
|---|---|
| date | Wed, 21 Nov 2012 12:55:30 -0500 |
| parents | ee072a7d271b |
| children | |
| files | galaxy_semwebtools sparql_import.xml |
| diffstat | 2 files changed, 11 insertions(+), 807 deletions(-) [+] |
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--- 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 @@ -<!DOCTYPE html> -<html lang="en"> -<head> - <meta charset="utf-8"> - <meta http-equiv="X-UA-Compatible" content="IE=edge" /> - <title> - saml / galaxy_semwebtools — Bitbucket -</title> - <link rel="icon" type="image/png" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/img/favicon.png"> - <meta id="bb-canon-url" name="bb-canon-url" content="https://bitbucket.org"> - - -<link rel="stylesheet" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/compressed/css/0def6d819f1a.css" type="text/css" /> - - <!--[if lt IE 9]><link rel="stylesheet" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/css/aui/aui-ie.css" media="all"><![endif]--> - <!--[if IE 9]><link rel="stylesheet" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/css/aui/aui-ie9.css" media="all"><![endif]--> - <!--[if IE]><link rel="stylesheet" href="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/css/aui-overrides-ie.css" media="all"><![endif]--> - 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Commits - </a> - </li> - - - <li> - <a href="/saml/galaxy_semwebtools/pull-requests" id="repo-pullrequests-link"> - Pull Requests - - - - </a> - </li> - - <li id="issues-tab" class=" - - hidden - - "> - <a href="/saml/galaxy_semwebtools/issues?status=new&status=open" id="repo-issues-link"> - Issues - - - - </a> - </li> - <li id="wiki-tab" class=" - - hidden - - "> - <a href="/saml/galaxy_semwebtools/wiki" id="repo-wiki-link">Wiki</a> - </li> - - <li> - <a href="/saml/galaxy_semwebtools/downloads" id="repo-downloads-link"> - Downloads - - - - </a> - </li> - - - </ul> - </div> - </nav> - - <div id="content" role="main"> - - <div id="repo-content"> - - <div id="repo-overview"> - - - - <div class="column"> - - - - <section id="readme"> - - <article class="readme file"> - <h1 id="semantic-web-tools-for-galaxy">Semantic Web Tools for Galaxy</h1> -<h2 id="sparql-import-tool">SPARQL Import tool</h2> -<p>This <a href="http://galaxyproject.org/">Galaxy (bioinformatics web portal)</a> 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.</p> -<h2 id="installation">Installation</h2> -<ol> -<li>Create a folder "semweb_tools" under [galaxy_root]/tools/ and add these files.</li> -<li>Add the following section right under the starting &lt;toolbox&gt; tag in [galaxy_root]/tool_conf.xml:</li> -</ol> -<div class="codehilite"><pre> <span class="nt"><section</span> <span class="na">name=</span><span class="s">"Semantic Web Tools"</span> <span class="na">id=</span><span class="s">"semweb_tools"</span><span class="nt">></span> - <span class="nt"><tool</span> <span class="na">file=</span><span class="s">"semweb_tools/sparql_import.xml"</span> <span class="nt">/></span> - <span class="nt"></section></span> -</pre></div> - - -<h2 id="change-log">Change log</h2> -<ul> -<li>2012-11-16: Now works properly (at least for my simple test case)!</li> -<li>2012-11-16: Created today, still under heavy development!</li> -</ul> - </article> - - </section> - - - - <section id="repo-activity"> - <h1> - Recent Activity - <a href="/saml/galaxy_semwebtools/rss" class="rss"><img src="https://dwz7u9t8u8usb.cloudfront.net/m/2219cd120e6a/img/icons/rss.png" alt="RSS feed for galaxy_semwebtools" title="RSS feed for galaxy_semwebtools" /></a> - </h1> - - - - - - - - - -<div class="newsfeed"> - - - - - - - - - <article class="news-item commit"> - <span class="icon commit"></span> - - - - <a href="/saml"><img alt="Samuel Lampa" src="https://secure.gravatar.com/avatar/87d770f5a0843a130b55572651e9d7d0?d=https%3A%2F%2Fdwz7u9t8u8usb.cloudfront.net%2Fm%2F2219cd120e6a%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> - 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--- 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 + <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> + </help> </tool>