workflow-to-galaxy 0.2.7 → 0.2.8

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Files changed (48) hide show
  1. data/CHANGES +6 -2
  2. data/README +11 -10
  3. data/Rakefile +7 -6
  4. data/doc/rdoc/CHANGES.html +105 -0
  5. data/doc/rdoc/Generator.html +262 -0
  6. data/doc/rdoc/LICENSE.html +115 -0
  7. data/doc/rdoc/README.html +167 -0
  8. data/doc/rdoc/WorkflowToGalaxy.html +135 -0
  9. data/doc/rdoc/created.rid +6 -1
  10. data/doc/rdoc/images/brick.png +0 -0
  11. data/doc/rdoc/images/brick_link.png +0 -0
  12. data/doc/rdoc/images/bug.png +0 -0
  13. data/doc/rdoc/images/bullet_black.png +0 -0
  14. data/doc/rdoc/images/bullet_toggle_minus.png +0 -0
  15. data/doc/rdoc/images/bullet_toggle_plus.png +0 -0
  16. data/doc/rdoc/images/date.png +0 -0
  17. data/doc/rdoc/images/find.png +0 -0
  18. data/doc/rdoc/images/loadingAnimation.gif +0 -0
  19. data/doc/rdoc/images/macFFBgHack.png +0 -0
  20. data/doc/rdoc/images/package.png +0 -0
  21. data/doc/rdoc/images/page_green.png +0 -0
  22. data/doc/rdoc/images/page_white_text.png +0 -0
  23. data/doc/rdoc/images/page_white_width.png +0 -0
  24. data/doc/rdoc/images/plugin.png +0 -0
  25. data/doc/rdoc/images/ruby.png +0 -0
  26. data/doc/rdoc/images/tag_green.png +0 -0
  27. data/doc/rdoc/images/wrench.png +0 -0
  28. data/doc/rdoc/images/wrench_orange.png +0 -0
  29. data/doc/rdoc/images/zoom.png +0 -0
  30. data/doc/rdoc/index.html +140 -20
  31. data/doc/rdoc/js/darkfish.js +116 -0
  32. data/doc/rdoc/js/jquery.js +32 -0
  33. data/doc/rdoc/js/quicksearch.js +114 -0
  34. data/doc/rdoc/js/thickbox-compressed.js +10 -0
  35. data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html +55 -0
  36. data/doc/rdoc/lib/workflow-to-galaxy_rb.html +54 -0
  37. data/doc/rdoc/rdoc.css +763 -0
  38. metadata +52 -14
  39. data/doc/rdoc/classes/Generator.html +0 -215
  40. data/doc/rdoc/classes/WorkflowToGalaxy.html +0 -105
  41. data/doc/rdoc/files/LICENSE.html +0 -133
  42. data/doc/rdoc/files/README.html +0 -192
  43. data/doc/rdoc/files/lib/workflow-to-galaxy/generator_rb.html +0 -108
  44. data/doc/rdoc/files/lib/workflow-to-galaxy_rb.html +0 -108
  45. data/doc/rdoc/fr_class_index.html +0 -28
  46. data/doc/rdoc/fr_file_index.html +0 -30
  47. data/doc/rdoc/fr_method_index.html +0 -28
  48. data/doc/rdoc/rdoc-style.css +0 -208
metadata CHANGED
@@ -1,13 +1,13 @@
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  --- !ruby/object:Gem::Specification
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  name: workflow-to-galaxy
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  version: !ruby/object:Gem::Version
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- hash: 25
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+ hash: 7
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  prerelease:
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  segments:
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  - 0
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  - 2
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- - 7
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- version: 0.2.7
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+ - 8
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+ version: 0.2.8
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  platform: ruby
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  authors:
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  - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-07-21 00:00:00 Z
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+ date: 2011-07-22 00:00:00 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: myexperiment-rest
@@ -65,6 +65,22 @@ dependencies:
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  version: 0.5.3
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  type: :runtime
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  version_requirements: *id003
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+ - !ruby/object:Gem::Dependency
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+ name: rubyzip
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+ prerelease: false
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+ requirement: &id004 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 51
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+ segments:
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+ - 0
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+ - 9
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+ - 4
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+ version: 0.9.4
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+ type: :runtime
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+ version_requirements: *id004
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  description: 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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  email: kostas.karasavvas@nbic.nl
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  executables:
@@ -83,18 +99,40 @@ files:
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  - bin/workflow_to_galaxy.rb
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  - lib/workflow-to-galaxy/generator.rb
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  - lib/workflow-to-galaxy.rb
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- - doc/rdoc/rdoc-style.css
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- - doc/rdoc/fr_file_index.html
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- - doc/rdoc/classes/WorkflowToGalaxy.html
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- - doc/rdoc/classes/Generator.html
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- - doc/rdoc/fr_class_index.html
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+ - doc/rdoc/WorkflowToGalaxy.html
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+ - doc/rdoc/rdoc.css
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+ - doc/rdoc/Generator.html
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+ - doc/rdoc/LICENSE.html
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  - doc/rdoc/index.html
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- - doc/rdoc/files/LICENSE.html
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- - doc/rdoc/files/README.html
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- - doc/rdoc/files/lib/workflow-to-galaxy_rb.html
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- - doc/rdoc/files/lib/workflow-to-galaxy/generator_rb.html
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- - doc/rdoc/fr_method_index.html
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+ - doc/rdoc/js/jquery.js
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+ - doc/rdoc/js/thickbox-compressed.js
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+ - doc/rdoc/js/darkfish.js
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+ - doc/rdoc/js/quicksearch.js
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+ - doc/rdoc/README.html
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+ - doc/rdoc/lib/workflow-to-galaxy_rb.html
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+ - doc/rdoc/lib/workflow-to-galaxy/generator_rb.html
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  - doc/rdoc/created.rid
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+ - doc/rdoc/CHANGES.html
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+ - doc/rdoc/images/find.png
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+ - doc/rdoc/images/bug.png
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+ - doc/rdoc/images/bullet_toggle_minus.png
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+ - doc/rdoc/images/wrench.png
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+ - doc/rdoc/images/bullet_black.png
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+ - doc/rdoc/images/macFFBgHack.png
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+ - doc/rdoc/images/page_white_text.png
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+ - doc/rdoc/images/ruby.png
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+ - doc/rdoc/images/bullet_toggle_plus.png
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+ - doc/rdoc/images/loadingAnimation.gif
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+ - doc/rdoc/images/brick.png
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+ - doc/rdoc/images/zoom.png
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+ - doc/rdoc/images/tag_green.png
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+ - doc/rdoc/images/page_green.png
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+ - doc/rdoc/images/brick_link.png
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+ - doc/rdoc/images/wrench_orange.png
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+ - doc/rdoc/images/date.png
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+ - doc/rdoc/images/page_white_width.png
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+ - doc/rdoc/images/package.png
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+ - doc/rdoc/images/plugin.png
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  homepage:
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  licenses: []
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data/doc/rdoc/classes/Generator.html DELETED
@@ -1,215 +0,0 @@
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- <?xml version="1.0" encoding="iso-8859-1"?>
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- <!DOCTYPE html
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- PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-
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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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- <title>Module: Generator</title>
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- <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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- <meta http-equiv="Content-Script-Type" content="text/javascript" />
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- <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
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- <script type="text/javascript">
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- // <![CDATA[
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-
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- function popupCode( url ) {
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- window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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- </head>
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- <body>
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- <div id="classHeader">
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- <table class="header-table">
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- <tr class="top-aligned-row">
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- <td><strong>Module</strong></td>
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- <td class="class-name-in-header">Generator</td>
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- </tr>
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- <tr class="top-aligned-row">
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- <td><strong>In:</strong></td>
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- <td>
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- <a href="../files/lib/workflow-to-galaxy/generator_rb.html">
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- lib/workflow-to-galaxy/generator.rb
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- </a>
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- <br />
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- </td>
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- </tr>
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-
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- </table>
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- </div>
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- <!-- banner header -->
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-
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- <div id="bodyContent">
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- <div id="contextContent">
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-
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- <div id="description">
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- <p>
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- The <a href="Generator.html">Generator</a> module contains two public
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- methods that generate a Galaxy&#8216;s tool XML and script files
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- </p>
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-
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- </div>
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-
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-
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- </div>
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-
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- <div id="method-list">
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- <h3 class="section-bar">Methods</h3>
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-
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- <div class="name-list">
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- <a href="#M000002">generate_script</a>&nbsp;&nbsp;
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- <a href="#M000001">generate_xml</a>&nbsp;&nbsp;
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- </div>
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- </div>
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- </div>
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- <div id="methods">
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- <h3 class="section-bar">Public Instance methods</h3>
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- <div id="method-M000002" class="method-detail">
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- <a name="M000002"></a>
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-
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- <div class="method-heading">
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- <a href="#M000002" class="method-signature">
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- <span class="method-name">Generator.generate_script(my_exp_rest, t2_server, script_file) &rarr; nil<br />
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- </span>
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- </a>
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- </div>
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-
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- <div class="method-description">
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- <p>
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- Generates the Galaxy tool&#8216;s script file responsible for talking to
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- the taverna server
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- </p>
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- <dl>
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- <dt><tt>my_exp_rest</tt></dt><dd>a <em>Workflow</em> object as returned from
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- <em>MyExperimentREST.ReadWorkflow.new(url)</em>
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-
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- </dd>
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- <dt><tt>t2_server</tt></dt><dd>a string containing the URL of the taverna 2 server
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-
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- </dd>
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- <dt><tt>script_out</tt></dt><dd>the file handler to write the generated script code
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-
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- </dd>
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- </dl>
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- <p><a class="source-toggle" href="#"
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- onclick="toggleCode('M000002-source');return false;">[Source]</a></p>
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- <div class="method-source-code" id="M000002-source">
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- <pre>
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- <span class="ruby-comment cmt"># File lib/workflow-to-galaxy/generator.rb, line 490</span>
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- 490: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate_script</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>, <span class="ruby-identifier">script_out</span>)
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- 491: <span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">script_out</span>)
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- 492: <span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">script_out</span>)
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- 493: <span class="ruby-identifier">script_create_t2_run</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">t2_server</span>)
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- 494: <span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
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- 495: <span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">script_out</span>)
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- 496: <span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
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- 497: <span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">script_out</span>)
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- 498: <span class="ruby-keyword kw">end</span>
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- </pre>
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- <span class="method-name">Generator.generate_xml(my_exp_rest, xml_file) &rarr; nil<br />
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- </span>
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- Generates the Galaxy tool&#8216;s xml file responsible for the UI.
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- <em>MyExperimentREST::Workflows.new.read(url)</em>
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- </dd>
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- <dt><tt>xml_file</tt></dt><dd>a string containing the name of the generated XML file
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- <dt><tt>xml_out</tt></dt><dd>the file handler to write the generated XML tags
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- <pre>
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- <span class="ruby-comment cmt"># File lib/workflow-to-galaxy/generator.rb, line 471</span>
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- 471: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">generate_xml</span>(<span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>, <span class="ruby-identifier">xml_out</span>)
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- 472: <span class="ruby-identifier">tool_begin_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">title</span>)
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- 473: <span class="ruby-identifier">command_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>, <span class="ruby-identifier">xml_file</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-value str">'.xml'</span>, <span class="ruby-value str">'.rb'</span>))
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- 474: <span class="ruby-identifier">inputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">inputs</span>)
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- 475: <span class="ruby-identifier">outputs_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>.<span class="ruby-identifier">outputs</span>)
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- 476: <span class="ruby-identifier">help_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>)
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- 477: <span class="ruby-identifier">tool_end_tag</span>(<span class="ruby-identifier">xml_out</span>)
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- 478: <span class="ruby-keyword kw">end</span>
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data/doc/rdoc/classes/WorkflowToGalaxy.html DELETED
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- <h1>LICENSE</h1>
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- <tr class="top-aligned-row">
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- <td><strong>Path:</strong></td>
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- <td>LICENSE
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- </td>
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- </tr>
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- <tr class="top-aligned-row">
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- <td><strong>Last Update:</strong></td>
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- <td>Wed Apr 06 16:41:53 +0200 2011</td>
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- <h2>workflow-to-galaxy</h2>
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- <p>
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- The MIT License
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- </p>
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- <p>
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- Copyright (c) 2010 - Netherlands Bioinformatics Centre
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- </p>
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- <p>
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- Permission is hereby granted, free of charge, to any person obtaining a
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- copy of this software and associated documentation files (the
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- &quot;Software&quot;), to deal in the Software without restriction,
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- including without limitation the rights to use, copy, modify, merge,
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- publish, distribute, sublicense, and/or sell copies of the Software, and to
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- permit persons to whom the Software is furnished to do so, subject to the
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- following conditions:
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- </p>
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- <p>
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- The above copyright notice and this permission notice shall be included in
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- all copies or substantial portions of the Software.
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- </p>
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- <p>
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- THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND,
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- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
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- NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
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- DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
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- OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
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- USE OR OTHER DEALINGS IN THE SOFTWARE.
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- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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