workflow-to-galaxy 0.2.7
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/CHANGES +6 -0
- data/LICENSE +23 -0
- data/README +60 -0
- data/Rakefile +54 -0
- data/bin/workflow_to_galaxy.rb +110 -0
- data/doc/rdoc/classes/Generator.html +215 -0
- data/doc/rdoc/classes/WorkflowToGalaxy.html +105 -0
- data/doc/rdoc/created.rid +1 -0
- data/doc/rdoc/files/LICENSE.html +133 -0
- data/doc/rdoc/files/README.html +192 -0
- data/doc/rdoc/files/lib/workflow-to-galaxy/generator_rb.html +108 -0
- data/doc/rdoc/files/lib/workflow-to-galaxy_rb.html +108 -0
- data/doc/rdoc/fr_class_index.html +28 -0
- data/doc/rdoc/fr_file_index.html +30 -0
- data/doc/rdoc/fr_method_index.html +28 -0
- data/doc/rdoc/index.html +24 -0
- data/doc/rdoc/rdoc-style.css +208 -0
- data/lib/workflow-to-galaxy.rb +5 -0
- data/lib/workflow-to-galaxy/generator.rb +497 -0
- metadata +132 -0
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<title>Module: WorkflowToGalaxy</title>
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<table class="header-table">
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<td><strong>Module</strong></td>
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<td class="class-name-in-header">WorkflowToGalaxy</td>
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<td><strong>In:</strong></td>
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<td>
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<a href="../files/lib/workflow-to-galaxy_rb.html">
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lib/workflow-to-galaxy.rb
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Thu, 21 Jul 2011 18:53:50 +0200
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<title>File: LICENSE</title>
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// ]]>
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<h1>LICENSE</h1>
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<td><strong>Path:</strong></td>
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<td>LICENSE
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<td><strong>Last Update:</strong></td>
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<td>Wed Apr 06 16:41:53 +0200 2011</td>
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<h2>workflow-to-galaxy</h2>
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The MIT License
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Copyright (c) 2010 - Netherlands Bioinformatics Centre
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Permission is hereby granted, free of charge, to any person obtaining a
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copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction,
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including without limitation the rights to use, copy, modify, merge,
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publish, distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to the
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following conditions:
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
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NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
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DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
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OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
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USE OR OTHER DEALINGS IN THE SOFTWARE.
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<h1>README</h1>
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<td>README
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<td>Thu Jul 21 18:53:40 +0200 2011</td>
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<h1>workflow-to-galaxy tool generator</h1>
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<tr><td valign="top">Authors:</td><td>Konstantinos Karasavvas
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</td></tr>
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<tr><td valign="top">Gem Version:</td><td>0.2.7
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</td></tr>
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<tr><td valign="top">Contact:</td><td><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a>
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<tr><td valign="top">Licence:</td><td>MIT (See LICENCE or <a
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href="http://www.opensource.org/licenses/mit-license">www.opensource.org/licenses/mit-license</a>)
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<tr><td valign="top">Copyright:</td><td>(c) 2010 Netherlands Bioinformatics Centre, The Netherlands
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</table>
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<h2>Synopsis</h2>
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<p>
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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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<h2>Installation</h2>
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workflow_to_galaxy [options] <myExperiement-workflow> |
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<t2flow-file>
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Generates a Galaxy tool (a UI xml definition plus a script) for the
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specified Taverna2 workflow, where <myExperiment-workflow> is the
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full URL of the workflow in the myExperiment website. Alternatively a
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t2flow file can be passed for workflows not in myExperiment. Available
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options are:
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href="http://localhost:8980/taverna-server">localhost:8980/taverna-server</a>"
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will be used.
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<h2>Example</h2>
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Let‘s say we want to install the taverna2 workflow <a
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href="http://www.myexperiment.org/workflows/74.html">www.myexperiment.org/workflows/74.html</a>
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from myExperiment repository:
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<tt>$ workflow_to_galaxy -s <a
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href="http://localhost:8980/taverna-server">localhost:8980/taverna-server</a>
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<a
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href="http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5">www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5</a></tt>
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<h2>References</h2>
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<td>lib/workflow-to-galaxy/generator.rb
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<td>Mon Jul 04 16:13:08 +0200 2011</td>
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<p>
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The <a href="../../../classes/Generator.html">Generator</a> module contains
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two public methods that generate a Galaxy‘s tool XML and script files
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