workflow-to-galaxy 0.3.4 → 0.3.5

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Files changed (14) hide show
  1. data/Rakefile +2 -2
  2. data/doc/rdoc/CHANGES.html +92 -89
  3. data/doc/rdoc/LICENSE.html +91 -89
  4. data/doc/rdoc/README.html +110 -107
  5. data/doc/rdoc/String.html +163 -148
  6. data/doc/rdoc/WorkflowToGalaxy.html +149 -121
  7. data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +227 -201
  8. data/doc/rdoc/WorkflowToGalaxy/Workflows.html +127 -115
  9. data/doc/rdoc/created.rid +7 -7
  10. data/doc/rdoc/index.html +87 -104
  11. data/doc/rdoc/js/darkfish.js +62 -99
  12. data/doc/rdoc/js/jquery.js +29 -15
  13. data/doc/rdoc/rdoc.css +339 -119
  14. metadata +101 -116
data/Rakefile CHANGED
@@ -7,7 +7,7 @@ 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 = '0.3.4'
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+ s.version = '0.3.5'
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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
@@ -18,7 +18,7 @@ spec = Gem::Specification.new do |s|
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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', '~> 0.3.0'
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+ s.add_dependency 'taverna-t2flow', '~> 0.4.0'
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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
@@ -1,92 +1,95 @@
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- <!DOCTYPE html>
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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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- <html>
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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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>CHANGES - workflow-to-galaxy Docs</title>
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+ <title>File: 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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-
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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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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
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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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- <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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-
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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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-
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- </ul>
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- </nav>
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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="project-metadata">
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+
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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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+ <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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+ </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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+ </div>
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  </div>
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- </nav>
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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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+ <div id="documentation">
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+
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+ <h1>Changes log for the Taverna-Galaxy Gem</h1>
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- <h2 id="label-Version+0.3.4">Version 0.3.4</h2>
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+ <h2>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 id="label-Version+0.3.3">Version 0.3.3</h2>
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+ <h2>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>
@@ -103,14 +106,14 @@ for auth</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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+ <h2>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 id="label-Version+0.3.1">Version 0.3.1</h2>
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+ <h2>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>
@@ -119,40 +122,40 @@ for auth</p>
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  <p>Extended workflow tests</p>
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  </li></ul>
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- <h2 id="label-Version+0.3.0">Version 0.3.0</h2>
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+ <h2>Version 0.3.0</h2>
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  <ul><li>
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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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+ <h2>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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+ <h2>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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  </li></ul>
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- <h2 id="label-Version+0.2.7">Version 0.2.7</h2>
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+ <h2>Version 0.2.7</h2>
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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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+ </div>
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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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+ <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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data/doc/rdoc/LICENSE.html CHANGED
@@ -1,116 +1,118 @@
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- <!DOCTYPE html>
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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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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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- <title>LICENSE - workflow-to-galaxy Docs</title>
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+ <title>File: 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/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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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet" />
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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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- <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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- <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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- <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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-
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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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- <h3 class="section-header">Class and Module Index</h3>
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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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- <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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- </ul>
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- </nav>
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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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+ <div id="project-metadata">
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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 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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+ <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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+ <li><a href="./String.html">String</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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+ <div id="documentation">
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+ <h2>workflow-to-galaxy</h2>
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  <p>The MIT License</p>
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  <p>Copyright © 2010 - Netherlands Bioinformatics Centre</p>
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  <p>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, including
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- without limitation the rights to use, copy, modify, merge, publish,
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- distribute, sublicense, and/or sell copies of the Software, and to permit
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- persons to whom the Software is furnished to do so, subject to the
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- following conditions:</p>
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+ copy of this software and associated documentation files (the “Software”),
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+ to deal in the Software without restriction, including without limitation
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+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
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+ and/or sell copies of the Software, and to permit persons to whom the
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+ Software is furnished to do so, subject to the following conditions:</p>
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  <p>The above copyright notice and this permission notice shall be included in
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  all copies or substantial portions of the Software.</p>
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- <p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
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- OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ <p>THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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  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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+ </body>
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+ </html>
116
118