workflow-to-galaxy 0.3.4 → 0.3.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/Rakefile +2 -2
- data/doc/rdoc/CHANGES.html +92 -89
- data/doc/rdoc/LICENSE.html +91 -89
- data/doc/rdoc/README.html +110 -107
- data/doc/rdoc/String.html +163 -148
- data/doc/rdoc/WorkflowToGalaxy.html +149 -121
- data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +227 -201
- data/doc/rdoc/WorkflowToGalaxy/Workflows.html +127 -115
- data/doc/rdoc/created.rid +7 -7
- data/doc/rdoc/index.html +87 -104
- data/doc/rdoc/js/darkfish.js +62 -99
- data/doc/rdoc/js/jquery.js +29 -15
- data/doc/rdoc/rdoc.css +339 -119
- metadata +101 -116
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<title>Module: WorkflowToGalaxy::Workflows</title>
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title="show/hide quicksearch" /></span></h3>
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<li><a href="../WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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<li><a href="../WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
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<li><a href="../WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
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<h1 class="module">WorkflowToGalaxy::Workflows</h1>
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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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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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<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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<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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<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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<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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