workflow-to-galaxy 0.3.4 → 0.3.5
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- data/Rakefile +2 -2
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- data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +227 -201
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README Fri, 23 Nov 2012 14:07:48 +0000
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LICENSE Fri, 23 Nov 2012 14:07:48 +0000
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CHANGES Fri, 23 Nov 2012 14:07:46 +0000
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lib/workflow-to-galaxy.rb Fri, 23 Nov 2012 14:07:47 +0000
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lib/workflow-to-galaxy/constants.rb Fri, 23 Nov 2012 14:07:47 +0000
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lib/workflow-to-galaxy/galaxy.rb Fri, 23 Nov 2012 14:07:47 +0000
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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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<div id="main">
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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, Finn Bacall</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>0.3.4</p>
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</td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
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<td>
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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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</td></tr><tr><td class="rdoc-term"><p>Licence</p></td>
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<td>
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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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<td>
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<p>© 2010 Netherlands Bioinformatics Centre, The Netherlands</p>
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<h2>Synopsis</h2>
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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
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is possible that it will support other workflow management systems in the
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future.</p>
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<h2>Installation</h2>
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<pre>[sudo] gem install workflow-to-galaxy</pre>
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<h2>Usage</h2>
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<p>workflow_to_galaxy [options] <myExperiement-workflow> |
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<t2flow-file></p>
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-t, --t2flow The workflow is a t2flow file.</pre>
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<h2>Example</h2>
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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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<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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<p><a href="http://galaxy.psu.edu">galaxy.psu.edu</a></p>
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</td></tr><tr><td class="rdoc-term"><p>Taverna2</p></td>
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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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<h2>Semantic Versioning</h2>
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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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<h2>Files</h2>
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<ul>
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<li class="file"><a href="CHANGES.html">CHANGES</a></li>
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<li class="file"><a href="LICENSE.html">LICENSE</a></li>
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</ul>
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<h2 id="classes">Classes/Modules</h2>
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<ul>
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<li class="module"><a href="WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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<li class="class"><a href="WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
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<li class="module"><a href="WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
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<li class="class"><a href="String.html">String</a></li>
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<h2 id="methods">Methods</h2>
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<li><a href="WorkflowToGalaxy/GalaxyTool.html#method-c-new">::new — WorkflowToGalaxy::GalaxyTool</a></li>
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<li><a href="WorkflowToGalaxy/GalaxyTool.html#method-i-generate">#generate — WorkflowToGalaxy::GalaxyTool</a></li>
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<li><a href="String.html#method-i-to_filename">#to_filename — String</a></li>
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<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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<p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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Rdoc Generator</a> 2</small>.</p>
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