workflow-to-galaxy 0.2.7 → 0.2.8

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Files changed (48) hide show
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+ <?xml version="1.0" encoding="utf-8"?>
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+ <title>File: README [workflow-to-galaxy Docs]</title>
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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
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+
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+ <script src="./js/jquery.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/thickbox-compressed.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="./js/quicksearch.js" type="text/javascript"
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+ <script src="./js/darkfish.js" type="text/javascript"
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+ <body class="file">
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+ <div id="metadata">
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+ <div id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="./index.html">Home</a>
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+ <a href="./index.html#classes">Classes</a>
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+ <a href="./index.html#methods">Methods</a>
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+ </h3>
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+ </div>
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+ </div>
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+ <div id="project-metadata">
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+ <div id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Files</h3>
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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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+ <li class="file"><a href="./README.html">README</a></li>
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+ </ul>
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+ </div>
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class Index
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+ <span class="search-toggle"><img src="./images/find.png"
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+ height="16" width="16" alt="[+]"
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+ title="show/hide quicksearch" /></span></h3>
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+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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+ <fieldset>
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+ <legend>Quicksearch</legend>
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+ <input type="text" name="quicksearch" value=""
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+ class="quicksearch-field" />
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+ </fieldset>
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+ </form>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="./Generator.html">Generator</a></li>
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+ <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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+
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+ </ul>
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+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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+ </div>
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="documentation">
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+
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+ <h1>workflow-to-galaxy tool generator</h1>
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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>0.2.8</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: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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+ <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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+ </td></tr></table>
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+
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+ <h2>Synopsis</h2>
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+
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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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+ execution of this workflow through Galaxy. The tool’s description is as
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+ good as the description provided in the workflow itself. Currently, the
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+ myExperiment workflow repository is used to access workflow information via
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+ its REST API but a workflow description from a file is also supported.</p>
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+
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+ <p>The name is workflow-to-galaxy rather than t2-workflow-to-galaxy because it
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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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+
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+ <h2>Installation</h2>
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+
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+ <pre>[sudo] gem install workflow-to-galaxy</pre>
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+
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+ <h2>Usage</h2>
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+
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+ <p>workflow_to_galaxy [options] &lt;myExperiement-workflow&gt; |
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+ &lt;t2flow-file&gt;</p>
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+
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+ <p>Generates a Galaxy tool (a UI xml definition plus a script) for the
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+ specified Taverna2 workflow, where &lt;myExperiment-workflow&gt; 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:</p>
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+
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+ <pre>-o OUTPUT, --output=OUTPUT The file name(s) of the generated tool. If it is not specified then the workflow's name will be used.
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+
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+ -s SERVER, --server=SERVER The taverna server that the script will request execution from. If it is not specified then &quot;http://localhost:8980/taverna-server&quot; will be used.
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+
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+ -t, --t2flow The workflow is a t2flow file.</pre>
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+
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+ <h2>Example</h2>
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+
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+ <p>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:</p>
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+
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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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+
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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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+ <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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+ <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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+ <td>
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+ <p><a href="http://www.taverna.org.uk">www.taverna.org.uk</a></p>
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+ </td></tr><tr><td class="rdoc-term"><p>myExperiment</p></td>
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+ <td>
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+ <p><a href="http://www.myexperiment.org">www.myexperiment.org</a></p>
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+ </td></tr></table>
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+
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+ </div>
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+
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+ <div id="validator-badges">
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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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+ </div>
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+ </body>
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+ </html>
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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+
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+ <title>Module: WorkflowToGalaxy</title>
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+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
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+ <script src="./js/jquery.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="./js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="./js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="./js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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+
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+ </head>
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+ <body id="top" class="module">
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+
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+ <div id="metadata">
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+ <div id="home-metadata">
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+ <div id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="./index.html">Home</a>
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+ <a href="./index.html#classes">Classes</a>
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+ <a href="./index.html#methods">Methods</a>
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+ </h3>
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+ </div>
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+ </div>
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+
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+ <div id="file-metadata">
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+ <div id="file-list-section" class="section">
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+ <h3 class="section-header">In Files</h3>
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+ <div class="section-body">
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+ <ul>
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+
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+ <li><a href="./lib/workflow-to-galaxy_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/workflow-to-galaxy.rb">lib/workflow-to-galaxy.rb</a></li>
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+
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+ </ul>
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+ <div id="class-metadata">
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+ </div>
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+ <div id="project-metadata">
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+
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+ <div id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Files</h3>
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+ <ul>
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+
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+ <li class="file"><a href="./CHANGES.html">CHANGES</a></li>
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+
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+ <li class="file"><a href="./LICENSE.html">LICENSE</a></li>
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+
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+ <li class="file"><a href="./README.html">README</a></li>
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+
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+ </ul>
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+ </div>
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+
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+
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class/Module Index
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+ <span class="search-toggle"><img src="./images/find.png"
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+ height="16" width="16" alt="[+]"
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+ title="show/hide quicksearch" /></span></h3>
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+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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+ <fieldset>
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+ <legend>Quicksearch</legend>
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+ <input type="text" name="quicksearch" value=""
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+ class="quicksearch-field" />
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+ </fieldset>
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+ </form>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="./Generator.html">Generator</a></li>
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+
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+ <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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+
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+ </ul>
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+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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+ </div>
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="documentation">
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+ <h1 class="module">WorkflowToGalaxy</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+
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+
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+ <div id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+
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+
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+
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+ <!-- Methods -->
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+
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+ </div><!-- 5Buntitled-5D -->
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+
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+
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+ </div><!-- documentation -->
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+
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+ <div id="validator-badges">
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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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+ </div>
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+
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+ </body>
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+ </html>
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+
data/doc/rdoc/created.rid CHANGED
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- Thu, 21 Jul 2011 18:53:50 +0200
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+ Fri, 22 Jul 2011 15:00:07 +0200
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+ lib/workflow-to-galaxy.rb Mon, 13 Dec 2010 15:22:40 +0100
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+ LICENSE Wed, 06 Apr 2011 16:41:53 +0200
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+ README Fri, 22 Jul 2011 14:51:41 +0200
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+ CHANGES Fri, 22 Jul 2011 14:46:31 +0200
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+ lib/workflow-to-galaxy/generator.rb Mon, 04 Jul 2011 16:13:08 +0200
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- PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
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- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
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+ <?xml version="1.0" encoding="UTF-8"?>
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-
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- workflow-to-galaxy Docs
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-
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- -->
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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+
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  <title>workflow-to-galaxy Docs</title>
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- <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+
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+ <link type="text/css" media="screen" href="rdoc.css" rel="stylesheet" />
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+
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+ <script src="js/jquery.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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- <frame src="files/README.html" name="docwin" />
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- </frameset>
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- </html>
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+ <body class="indexpage">
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+
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+
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+ <h1>workflow-to-galaxy Docs</h1>
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+
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+
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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>0.2.8</p>
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+ </td></tr><tr><td class="rdoc-term"><p>Contact</p></td>
34
+ <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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+ <p>MIT (See LICENCE or <a
39
+ 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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+ </td></tr></table>
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+
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+ <h2>Synopsis</h2>
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+
47
+ <p>This script requires a Taverna2 workflow URL as input and generates a
48
+ Galaxy tool (a UI XML definition plus a script) that will enable the
49
+ execution of this workflow through Galaxy. The tool’s description is as
50
+ good as the description provided in the workflow itself. Currently, the
51
+ myExperiment workflow repository is used to access workflow information via
52
+ its REST API but a workflow description from a file is also supported.</p>
53
+
54
+ <p>The name is workflow-to-galaxy rather than t2-workflow-to-galaxy because it
55
+ is possible that it will support other workflow management systems in the
56
+ future.</p>
57
+
58
+ <h2>Installation</h2>
59
+
60
+ <pre>[sudo] gem install workflow-to-galaxy</pre>
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+
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+ <h2>Usage</h2>
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+
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+ <p>workflow_to_galaxy [options] &lt;myExperiement-workflow&gt; |
65
+ &lt;t2flow-file&gt;</p>
66
+
67
+ <p>Generates a Galaxy tool (a UI xml definition plus a script) for the
68
+ specified Taverna2 workflow, where &lt;myExperiment-workflow&gt; is the
69
+ full URL of the workflow in the myExperiment website. Alternatively a
70
+ t2flow file can be passed for workflows not in myExperiment. Available
71
+ options are:</p>
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+
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+ <pre>-o OUTPUT, --output=OUTPUT The file name(s) of the generated tool. If it is not specified then the workflow's name will be used.
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+
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+ -s SERVER, --server=SERVER The taverna server that the script will request execution from. If it is not specified then &quot;http://localhost:8980/taverna-server&quot; will be used.
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+
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+ -t, --t2flow The workflow is a t2flow file.</pre>
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+
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+ <h2>Example</h2>
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+
81
+ <p>Let’s say we want to install the taverna2 workflow <a
82
+ href="http://www.myexperiment.org/workflows/74.html">www.myexperiment.org/workflows/74.html</a>
83
+ from myExperiment repository:</p>
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+
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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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+
87
+ <h2>References</h2>
88
+ <table class="rdoc-list"><tr><td class="rdoc-term"><p>Taverna-Galaxy</p></td>
89
+ <td>
90
+ <p><a
91
+ href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">trac.nbic.nl/elabfactory/wiki/eGalaxy</a></p>
92
+ </td></tr><tr><td class="rdoc-term"><p>Galaxy</p></td>
93
+ <td>
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+ <p><a href="http://galaxy.psu.edu">galaxy.psu.edu</a></p>
95
+ </td></tr><tr><td class="rdoc-term"><p>Taverna2</p></td>
96
+ <td>
97
+ <p><a href="http://www.taverna.org.uk">www.taverna.org.uk</a></p>
98
+ </td></tr><tr><td class="rdoc-term"><p>myExperiment</p></td>
99
+ <td>
100
+ <p><a href="http://www.myexperiment.org">www.myexperiment.org</a></p>
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+ </td></tr></table>
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+
103
+ </div>
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+
105
+
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+
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+
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+ <h2>Files</h2>
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+ <ul>
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+
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+ <li class="file"><a href="CHANGES.html">CHANGES</a></li>
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+
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+ <li class="file"><a href="LICENSE.html">LICENSE</a></li>
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+
115
+ <li class="file"><a href="README.html">README</a></li>
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+
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+ </ul>
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+
119
+
120
+ <h2 id="classes">Classes/Modules</h2>
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+ <ul>
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+
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+ <li class="module"><a href="Generator.html">Generator</a></li>
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+
125
+ <li class="module"><a href="WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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+
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+ </ul>
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+
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+ <h2 id="methods">Methods</h2>
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+ <ul>
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+
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+ <li><a href="Generator.html#method-i-generate_script">#generate_script &mdash; Generator</a></li>
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+
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+ <li><a href="Generator.html#method-i-generate_xml">#generate_xml &mdash; Generator</a></li>
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+
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+ </ul>
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+
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+ <div id="validator-badges">
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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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+ </div>
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+ </body>
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+ </html>
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+ /**
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+ *
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+ * Darkfish Page Functions
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+ * $Id: darkfish.js 53 2009-01-07 02:52:03Z deveiant $
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+ *
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+ * Author: Michael Granger <mgranger@laika.com>
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+ *
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+ */
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+
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+ /* Provide console simulation for firebug-less environments */
11
+ if (!("console" in window) || !("firebug" in console)) {
12
+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
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+ "group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"];
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+
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+ window.console = {};
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+ for (var i = 0; i < names.length; ++i)
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+ window.console[names[i]] = function() {};
18
+ };
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+
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+
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+ /**
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+ * Unwrap the first element that matches the given @expr@ from the targets and return them.
23
+ */
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+ $.fn.unwrap = function( expr ) {
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+ return this.each( function() {
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+ $(this).parents( expr ).eq( 0 ).after( this ).remove();
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+ });
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+ };
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+
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+
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+ function showSource( e ) {
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+ var codeSections = $(target).
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+ parents('.method-detail').
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+ find('.method-source-code');
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+
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+ parents('.method-detail').
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+ find('.method-source-code').
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+ slideToggle();
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+ };
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+
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+ function hookSourceViews() {
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+ $('.method-description,.method-heading').click( showSource );
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+ };
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+
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+ function toggleDebuggingSection() {
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+ $('.debugging-section').slideToggle();
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+ };
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+
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+ function hookDebuggingToggle() {
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+ $('#debugging-toggle img').click( toggleDebuggingSection );
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+ };
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+
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+ function hookQuickSearch() {
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+ $('.quicksearch-field').each( function() {
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+ var searchElems = $(this).parents('.section').find( 'li' );
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+ var toggle = $(this).parents('.section').find('h3 .search-toggle');
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+ // console.debug( "Toggle is: %o", toggle );
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+ var qsbox = $(this).parents('form').get( 0 );
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+
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+ $(this).quicksearch( this, searchElems, {
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+ noSearchResultsIndicator: 'no-class-search-results',
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+ focusOnLoad: false
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+ });
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+ $(toggle).click( function() {
67
+ // console.debug( "Toggling qsbox: %o", qsbox );
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+ $(qsbox).toggle();
69
+ });
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+ });
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+ };
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+
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+ function highlightTarget( anchor ) {
74
+ console.debug( "Highlighting target '%s'.", anchor );
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+
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+ $("a[name=" + anchor + "]").each( function() {
77
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80
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81
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83
+ }
84
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85
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+
87
+ function highlightLocationTarget() {
88
+ console.debug( "Location hash: %s", window.location.hash );
89
+ if ( ! window.location.hash || window.location.hash.length == 0 ) return;
90
+
91
+ var anchor = window.location.hash.substring(1);
92
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93
+
94
+ highlightTarget( anchor );
95
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+
97
+ function highlightClickTarget( event ) {
98
+ console.debug( "Highlighting click target for event %o", event.target );
99
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100
+ var anchor = $(event.target).attr( 'href' ).substring(1);
101
+ console.debug( "Found target anchor: %s", anchor );
102
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103
+ } catch ( err ) {
104
+ console.error( "Exception while highlighting: %o", err );
105
+ };
106
+ };
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+
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+
109
+ $(document).ready( function() {
110
+ hookSourceViews();
111
+ hookDebuggingToggle();
112
+ hookQuickSearch();
113
+ highlightLocationTarget();
114
+
115
+ $('ul.link-list a').bind( "click", highlightClickTarget );
116
+ });