workflow-to-galaxy 0.3.3 → 0.3.4

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@@ -1,7 +1,7 @@
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- Mon, 16 Jan 2012 16:21:48 +0100
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- lib/workflow-to-galaxy.rb Tue, 15 Nov 2011 15:48:17 +0100
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- lib/workflow-to-galaxy/constants.rb Mon, 10 Oct 2011 14:10:32 +0200
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- lib/workflow-to-galaxy/galaxy.rb Mon, 16 Jan 2012 14:03:11 +0100
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- LICENSE Tue, 26 Jul 2011 16:35:55 +0200
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- README Thu, 12 Jan 2012 14:58:21 +0100
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- CHANGES Mon, 16 Jan 2012 16:21:32 +0100
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+ Wed, 10 Oct 2012 15:44:48 +0100
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+ lib/workflow-to-galaxy/constants.rb Tue, 09 Oct 2012 14:23:30 +0100
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+ lib/workflow-to-galaxy/galaxy.rb Tue, 09 Oct 2012 14:23:30 +0100
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+ lib/workflow-to-galaxy.rb Tue, 09 Oct 2012 14:23:30 +0100
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+ LICENSE Tue, 09 Oct 2012 14:23:30 +0100
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+ README Wed, 10 Oct 2012 15:39:47 +0100
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- <div id="main">
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-
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- <table class="rdoc-list"><tr><td class="rdoc-term"><p>Authors</p></td>
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- <td>
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- <p>Konstantinos Karasavvas</p>
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- </td></tr><tr><td class="rdoc-term"><p>Gem Version</p></td>
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- <td>
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- <p>0.3.3</p>
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- </td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
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- <p><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a></p>
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- </td></tr><tr><td class="rdoc-term"><p>Licence</p></td>
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- <td>
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+ <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a>
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+ <div id="documentation" class="description">
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+
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+ <h1 id="label-workflow-to-galaxy+tool+generator">workflow-to-galaxy tool generator</h1>
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+ <dl class="rdoc-list note-list"><dt>Authors
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+ <dd>
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+ <p>Konstantinos Karasavvas, Finn Bacall</p>
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+ </dd><dt>Gem Version
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+ <dd>
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+ <p>0.3.4</p>
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+ </dd><dt>Contact
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+ <dd>
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+ <p><a href="mailto:r.m.van_schouwen@lumc.nl">r.m.van_schouwen@lumc.nl</a>, <a
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+ href="mailto:finn.bacall@cs.man.ac.uk">finn.bacall@cs.man.ac.uk</a></p>
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  <p>MIT (See LICENCE or <a
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  href="http://www.opensource.org/licenses/mit-license">www.opensource.org/licenses/mit-license</a>)</p>
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- </td></tr><tr><td class="rdoc-term"><p>Copyright</p></td>
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+ </dd><dt>Copyright
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  <p>© 2010 Netherlands Bioinformatics Centre, The Netherlands</p>
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  <p>This script requires a Taverna2 workflow URL as input and generates a
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  Galaxy tool (a UI XML definition plus a script) that will enable the
@@ -55,11 +112,11 @@ its REST API but a workflow description from a file is also supported.</p>
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  is possible that it will support other workflow management systems in the
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  <pre>[sudo] gem install workflow-to-galaxy</pre>
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  &lt;t2flow-file&gt;</p>
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  -t, --t2flow The workflow is a t2flow file.</pre>
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  <p>Let’s say we want to install the taverna2 workflow <a
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  <pre>$ workflow_to_galaxy -s http://localhost:8980/taverna-server http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5</pre>
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- <h2>References</h2>
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- <table class="rdoc-list"><tr><td class="rdoc-term"><p>Taverna-Galaxy</p></td>
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- <td>
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+ <h2 id="label-References">References</h2>
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+ <dl class="rdoc-list note-list"><dt>Taverna-Galaxy
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+ <dd>
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  <p><a
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  href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">trac.nbic.nl/elabfactory/wiki/eGalaxy</a></p>
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- </td></tr><tr><td class="rdoc-term"><p>Galaxy</p></td>
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+ </dd><dt>Galaxy
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  <p><a href="http://galaxy.psu.edu">galaxy.psu.edu</a></p>
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  <p><a href="http://www.taverna.org.uk">www.taverna.org.uk</a></p>
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  <p><a href="http://www.myexperiment.org">www.myexperiment.org</a></p>
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  <p>This module uses semantic versioning concepts from <a
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  href="http://semver.org/.">semver.org/.</a></p>
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