workflow-to-galaxy 0.3.3 → 0.3.4

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Files changed (35) hide show
  1. data/CHANGES +3 -0
  2. data/README +3 -3
  3. data/Rakefile +4 -4
  4. data/doc/rdoc/CHANGES.html +93 -91
  5. data/doc/rdoc/LICENSE.html +81 -84
  6. data/doc/rdoc/README.html +112 -114
  7. data/doc/rdoc/String.html +148 -161
  8. data/doc/rdoc/WorkflowToGalaxy.html +122 -148
  9. data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +203 -229
  10. data/doc/rdoc/WorkflowToGalaxy/Workflows.html +115 -125
  11. data/doc/rdoc/created.rid +7 -7
  12. data/doc/rdoc/images/add.png +0 -0
  13. data/doc/rdoc/images/delete.png +0 -0
  14. data/doc/rdoc/images/tag_blue.png +0 -0
  15. data/doc/rdoc/images/transparent.png +0 -0
  16. data/doc/rdoc/index.html +108 -90
  17. data/doc/rdoc/js/darkfish.js +99 -62
  18. data/doc/rdoc/js/jquery.js +15 -29
  19. data/doc/rdoc/js/navigation.js +142 -0
  20. data/doc/rdoc/js/search.js +94 -0
  21. data/doc/rdoc/js/search_index.js +1 -0
  22. data/doc/rdoc/js/searcher.js +228 -0
  23. data/doc/rdoc/rdoc.css +119 -339
  24. data/doc/rdoc/table_of_contents.html +103 -0
  25. metadata +44 -42
  26. data/doc/rdoc/Generator.html +0 -262
  27. data/doc/rdoc/Object.html +0 -161
  28. data/doc/rdoc/js/quicksearch.js +0 -114
  29. data/doc/rdoc/js/thickbox-compressed.js +0 -10
  30. data/doc/rdoc/lib/generator_rb.html +0 -54
  31. data/doc/rdoc/lib/workflow-to-galaxy/constants_rb.html +0 -52
  32. data/doc/rdoc/lib/workflow-to-galaxy/galaxy_rb.html +0 -58
  33. data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html +0 -58
  34. data/doc/rdoc/lib/workflow-to-galaxy_rb.html +0 -56
  35. data/doc/rdoc/lib/workflow_to_galaxy_rb.html +0 -60
data/CHANGES CHANGED
@@ -1,5 +1,8 @@
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  = Changes log for the Taverna-Galaxy Gem
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+ == Version 0.3.4
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+ * Updated taverna-t2flow dependency to 0.3.0
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+
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  == Version 0.3.3
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  * Multiline output examples are now displayed better in HTML/Galaxy (similar to inputs)
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  * Updated wkf 74 test
data/README CHANGED
@@ -1,9 +1,9 @@
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  = workflow-to-galaxy tool generator
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- Authors:: Konstantinos Karasavvas
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- Gem Version:: 0.3.3
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- Contact:: mailto:kostas.karasavvas@nbic.nl
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+ Authors:: Konstantinos Karasavvas, Finn Bacall
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+ Gem Version:: 0.3.4
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+ Contact:: mailto:r.m.van_schouwen@lumc.nl, mailto:finn.bacall@cs.man.ac.uk
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  Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
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  Copyright:: (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
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data/Rakefile CHANGED
@@ -7,18 +7,18 @@ require 'rdoc/task'
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  spec = Gem::Specification.new do |s|
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  s.name = 'workflow-to-galaxy'
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- s.version = '0.3.3'
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+ s.version = '0.3.4'
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  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
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  s.summary = 'This script acquires information for a taverna 2 workflow from myExperiment (or from a file) and generates a Galaxy tool (.xml and .rb files).'
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  s.description = s.summary
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- s.author = 'Kostas Karasavvas'
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- s.email = 'kostas.karasavvas@nbic.nl'
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+ s.authors = ['Kostas Karasavvas', 'Finn Bacall']
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+ s.email = ["finn.bacall@cs.man.ac.uk", "R.M.van_Schouwen@lumc.nl"]
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  s.executables = ['workflow_to_galaxy.rb']
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  s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,doc,spec}/**/*")
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  s.require_path = "lib"
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  s.bindir = "bin"
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  s.add_dependency 'myexperiment-rest', '~> 0.3.0'
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- s.add_dependency 'taverna-t2flow', '~> 0.2.0'
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+ s.add_dependency 'taverna-t2flow', '~> 0.3.0'
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  s.add_dependency 't2-server', '~> 0.6.1'
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  s.add_dependency 'rubyzip', '~> 0.9.4'
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  end
data/doc/rdoc/CHANGES.html CHANGED
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- <?xml version="1.0" encoding="utf-8"?>
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- <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <!DOCTYPE html>
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- <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <html>
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  <head>
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- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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- <title>File: CHANGES [workflow-to-galaxy Docs]</title>
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+ <title>CHANGES - workflow-to-galaxy Docs</title>
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- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "./";
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+ </script>
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+
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+ <script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
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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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- charset="utf-8"></script>
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- <script src="./js/darkfish.js" type="text/javascript"
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- charset="utf-8"></script>
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- </head>
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  <body class="file">
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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="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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- <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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- <li class="file"><a href="./README.html">README</a></li>
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- </ul>
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- </div>
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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 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="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
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-
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- <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
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-
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- <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
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-
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- <li><a href="./String.html">String</a></li>
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-
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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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+ <nav id="metadata">
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+ <nav 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="./table_of_contents.html#classes">Classes</a>
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+ <a href="./table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+
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+
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+
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+
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+ <div id="project-metadata">
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+
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+ <ul>
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+
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+ <li class="file"><a href="./CHANGES.html">CHANGES</a>
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+
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+ <li class="file"><a href="./LICENSE.html">LICENSE</a>
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+
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+ <li class="file"><a href="./README.html">README</a>
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+
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+ </ul>
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+ </nav>
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+
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a>
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+
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+ <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a>
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+
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+ <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a>
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+
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+ <li><a href="./String.html">String</a>
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+
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+ </ul>
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+ </nav>
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+
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  </div>
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+ </nav>
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- <div id="documentation">
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-
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- <h1>Changes log for the Taverna-Galaxy Gem</h1>
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+ <div id="documentation" class="description">
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+
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+ <h1 id="label-Changes+log+for+the+Taverna-Galaxy+Gem">Changes log for the Taverna-Galaxy Gem</h1>
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+
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+ <h2 id="label-Version+0.3.4">Version 0.3.4</h2>
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+ <ul><li>
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+ <p>Updated taverna-t2flow dependency to 0.3.0</p>
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+ </li></ul>
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- <h2>Version 0.3.3</h2>
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+ <h2 id="label-Version+0.3.3">Version 0.3.3</h2>
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  <ul><li>
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  <p>Multiline output examples are now displayed better in HTML/Galaxy (similar
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  to inputs)</p>
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  </li></ul>
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  </li></ul>
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+ <h2 id="label-Version+0.3.2">Version 0.3.2</h2>
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  <ul><li>
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  <p>Automatic filename creation is more robust (all special chars are removed)</p>
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  </li><li>
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  <p>More workflow tests</p>
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  </li></ul>
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- <h2>Version 0.3.1</h2>
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+ <h2 id="label-Version+0.3.1">Version 0.3.1</h2>
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  <ul><li>
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  <p>Used semver formally (taged: v0.3.1 semver)</p>
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  </li><li>
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  <p>Extended workflow tests</p>
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+ <h2 id="label-Version+0.3.0">Version 0.3.0</h2>
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  <p>Updated to newer myexperiment-rest lib (0.3.0).</p>
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  </li><li>
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  <p>Restructured, now more modular and extensible.</p>
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  </li></ul>
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+ <h2 id="label-Version+0.2.9">Version 0.2.9</h2>
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  <ul><li>
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  <p>Fixed minor bug when workflow had empty description</p>
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  </li><li>
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  <p>Added instructions to generated scripts on how to run them without Galaxy.</p>
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  </li></ul>
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+ <h2 id="label-Version+0.2.8">Version 0.2.8</h2>
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  <ul><li>
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  <p>Clean up of documentation</p>
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  </li><li>
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  <p>Added rubyzip dependency to gemspec</p>
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  <ul><li>
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  <p>A Galaxy tool can now also be created by providing a t2flow file with the
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  –t2flow flag.</p>
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  </li></ul>
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+ </div>
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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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- </body>
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- </html>
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+
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+ <footer id="validator-badges">
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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data/doc/rdoc/LICENSE.html CHANGED
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- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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+ <title>LICENSE - 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 type="text/javascript">
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+ var rdoc_rel_prefix = "./";
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
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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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- <ul>
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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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- <li class="file"><a href="./README.html">README</a></li>
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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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- <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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- <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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+ <nav id="metadata">
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+ <nav 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="./table_of_contents.html#classes">Classes</a>
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+ <a href="./table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+ <div id="project-metadata">
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+ <ul>
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+ <li class="file"><a href="./CHANGES.html">CHANGES</a>
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+ <li class="file"><a href="./LICENSE.html">LICENSE</a>
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+ <li class="file"><a href="./README.html">README</a>
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+ </ul>
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+ </nav>
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a>
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+
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+ <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a>
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+ <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a>
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+ <li><a href="./String.html">String</a>
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+ </nav>
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  </div>
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+ </nav>
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- <div id="documentation">
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- <h2>workflow-to-galaxy</h2>
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+ <div id="documentation" class="description">
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+ <h2 id="label-workflow-to-galaxy">workflow-to-galaxy</h2>
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  <p>The MIT License</p>
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@@ -107,13 +104,13 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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  DEALINGS IN THE SOFTWARE.</p>
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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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+ <footer id="validator-badges">
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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