workflow-to-galaxy 0.3.4 → 0.3.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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@@ -1,7 +1,7 @@
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- Wed, 10 Oct 2012 15:44:48 +0100
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- lib/workflow-to-galaxy/constants.rb Tue, 09 Oct 2012 14:23:30 +0100
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- lib/workflow-to-galaxy/galaxy.rb Tue, 09 Oct 2012 14:23:30 +0100
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- lib/workflow-to-galaxy.rb Tue, 09 Oct 2012 14:23:30 +0100
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- LICENSE Tue, 09 Oct 2012 14:23:30 +0100
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- README Wed, 10 Oct 2012 15:39:47 +0100
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- CHANGES Wed, 10 Oct 2012 15:38:18 +0100
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+ README Fri, 23 Nov 2012 14:07:48 +0000
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+ CHANGES Fri, 23 Nov 2012 14:07:46 +0000
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+ lib/workflow-to-galaxy.rb Fri, 23 Nov 2012 14:07:47 +0000
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+ lib/workflow-to-galaxy/constants.rb Fri, 23 Nov 2012 14:07:47 +0000
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+ lib/workflow-to-galaxy/galaxy.rb Fri, 23 Nov 2012 14:07:47 +0000
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- <h1 id="label-workflow-to-galaxy+tool+generator">workflow-to-galaxy tool generator</h1>
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- <dl class="rdoc-list note-list"><dt>Authors
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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, Finn Bacall</p>
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  <p>0.3.4</p>
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  <p><a href="mailto:r.m.van_schouwen@lumc.nl">r.m.van_schouwen@lumc.nl</a>, <a
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  <p>MIT (See LICENCE or <a
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+ </td></tr><tr><td class="rdoc-term"><p>Copyright</p></td>
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  <p>© 2010 Netherlands Bioinformatics Centre, The Netherlands</p>
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  <p>This script requires a Taverna2 workflow URL as input and generates a
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