RubyGems - workflow-to-galaxy - Versions diffs - 0.2.7 → 0.2.8 - Mend

workflow-to-galaxy 0.2.7 → 0.2.8

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.

Files changed (48) hide show

data/CHANGES +6 -2
data/README +11 -10
data/Rakefile +7 -6
data/doc/rdoc/CHANGES.html +105 -0
data/doc/rdoc/Generator.html +262 -0
data/doc/rdoc/LICENSE.html +115 -0
data/doc/rdoc/README.html +167 -0
data/doc/rdoc/WorkflowToGalaxy.html +135 -0
data/doc/rdoc/created.rid +6 -1
data/doc/rdoc/images/brick.png +0 -0
data/doc/rdoc/images/brick_link.png +0 -0
data/doc/rdoc/images/bug.png +0 -0
data/doc/rdoc/images/bullet_black.png +0 -0
data/doc/rdoc/images/bullet_toggle_minus.png +0 -0
data/doc/rdoc/images/bullet_toggle_plus.png +0 -0
data/doc/rdoc/images/date.png +0 -0
data/doc/rdoc/images/find.png +0 -0
data/doc/rdoc/images/loadingAnimation.gif +0 -0
data/doc/rdoc/images/macFFBgHack.png +0 -0
data/doc/rdoc/images/package.png +0 -0
data/doc/rdoc/images/page_green.png +0 -0
data/doc/rdoc/images/page_white_text.png +0 -0
data/doc/rdoc/images/page_white_width.png +0 -0
data/doc/rdoc/images/plugin.png +0 -0
data/doc/rdoc/images/ruby.png +0 -0
data/doc/rdoc/images/tag_green.png +0 -0
data/doc/rdoc/images/wrench.png +0 -0
data/doc/rdoc/images/wrench_orange.png +0 -0
data/doc/rdoc/images/zoom.png +0 -0
data/doc/rdoc/index.html +140 -20
data/doc/rdoc/js/darkfish.js +116 -0
data/doc/rdoc/js/jquery.js +32 -0
data/doc/rdoc/js/quicksearch.js +114 -0
data/doc/rdoc/js/thickbox-compressed.js +10 -0
data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html +55 -0
data/doc/rdoc/lib/workflow-to-galaxy_rb.html +54 -0
data/doc/rdoc/rdoc.css +763 -0
metadata +52 -14
data/doc/rdoc/classes/Generator.html +0 -215
data/doc/rdoc/classes/WorkflowToGalaxy.html +0 -105
data/doc/rdoc/files/LICENSE.html +0 -133
data/doc/rdoc/files/README.html +0 -192
data/doc/rdoc/files/lib/workflow-to-galaxy/generator_rb.html +0 -108
data/doc/rdoc/files/lib/workflow-to-galaxy_rb.html +0 -108
data/doc/rdoc/fr_class_index.html +0 -28
data/doc/rdoc/fr_file_index.html +0 -30
data/doc/rdoc/fr_method_index.html +0 -28
data/doc/rdoc/rdoc-style.css +0 -208

metadata CHANGED Viewed

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: workflow-to-galaxy
 version: !ruby/object:Gem::Version
-  hash: 25
+  hash: 7
   prerelease:
   segments:
   - 0
   - 2
-  - 7
-  version: 0.2.7
+  - 8
+  version: 0.2.8
 platform: ruby
 authors:
 - Kostas Karasavvas
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
-date: 2011-07-21 00:00:00 Z
+date: 2011-07-22 00:00:00 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: myexperiment-rest
@@ -65,6 +65,22 @@ dependencies:
         version: 0.5.3
   type: :runtime
   version_requirements: *id003
+- !ruby/object:Gem::Dependency
+  name: rubyzip
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        hash: 51
+        segments:
+        - 0
+        - 9
+        - 4
+        version: 0.9.4
+  type: :runtime
+  version_requirements: *id004
 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).
 email: kostas.karasavvas@nbic.nl
 executables:
@@ -83,18 +99,40 @@ files:
 - bin/workflow_to_galaxy.rb
 - lib/workflow-to-galaxy/generator.rb
 - lib/workflow-to-galaxy.rb
-- doc/rdoc/rdoc-style.css
-- doc/rdoc/fr_file_index.html
-- doc/rdoc/classes/WorkflowToGalaxy.html
-- doc/rdoc/classes/Generator.html
-- doc/rdoc/fr_class_index.html
+- doc/rdoc/WorkflowToGalaxy.html
+- doc/rdoc/rdoc.css
+- doc/rdoc/Generator.html
+- doc/rdoc/LICENSE.html
 - doc/rdoc/index.html
-- doc/rdoc/files/LICENSE.html
-- doc/rdoc/files/README.html
-- doc/rdoc/files/lib/workflow-to-galaxy_rb.html
-- doc/rdoc/files/lib/workflow-to-galaxy/generator_rb.html
-- doc/rdoc/fr_method_index.html
+- doc/rdoc/js/jquery.js
+- doc/rdoc/js/thickbox-compressed.js
+- doc/rdoc/js/darkfish.js
+- doc/rdoc/js/quicksearch.js
+- doc/rdoc/README.html
+- doc/rdoc/lib/workflow-to-galaxy_rb.html
+- doc/rdoc/lib/workflow-to-galaxy/generator_rb.html
 - doc/rdoc/created.rid
+- doc/rdoc/CHANGES.html
+- doc/rdoc/images/find.png
+- doc/rdoc/images/bug.png
+- doc/rdoc/images/bullet_toggle_minus.png
+- doc/rdoc/images/wrench.png
+- doc/rdoc/images/bullet_black.png
+- doc/rdoc/images/macFFBgHack.png
+- doc/rdoc/images/page_white_text.png
+- doc/rdoc/images/ruby.png
+- doc/rdoc/images/bullet_toggle_plus.png
+- doc/rdoc/images/loadingAnimation.gif
+- doc/rdoc/images/brick.png
+- doc/rdoc/images/zoom.png
+- doc/rdoc/images/tag_green.png
+- doc/rdoc/images/page_green.png
+- doc/rdoc/images/brick_link.png
+- doc/rdoc/images/wrench_orange.png
+- doc/rdoc/images/date.png
+- doc/rdoc/images/page_white_width.png
+- doc/rdoc/images/package.png
+- doc/rdoc/images/plugin.png
 homepage:
 licenses: []

data/doc/rdoc/classes/Generator.html DELETED Viewed

@@ -1,215 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>Module: Generator</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-    elemStyle = elem.style;
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-    return true;
-  }
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  // ]]>
-  </script>
-</head>
-<body>
-    <div id="classHeader">
-        <table class="header-table">
-        <tr class="top-aligned-row">
-          <td><strong>Module</strong></td>
-          <td class="class-name-in-header">Generator</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <a href="../files/lib/workflow-to-galaxy/generator_rb.html">
-                lib/workflow-to-galaxy/generator.rb
-                </a>
-        <br />
-            </td>
-        </tr>
-        </table>
-    </div>
-  <!-- banner header -->
-  <div id="bodyContent">
-  <div id="contextContent">
-    <div id="description">
-      <p>
-The <a href="Generator.html">Generator</a> module contains two public
-methods that generate a Galaxy&#8216;s tool XML and script files
-</p>
-    </div>
-   </div>
-    <div id="method-list">
-      <h3 class="section-bar">Methods</h3>
-      <div class="name-list">
-      <a href="#M000002">generate_script</a>&nbsp;&nbsp;
-      <a href="#M000001">generate_xml</a>&nbsp;&nbsp;
-      </div>
-    </div>
-  </div>
-    <!-- if includes -->
-    <div id="section">
-    <!-- if method_list -->
-    <div id="methods">
-      <h3 class="section-bar">Public Instance methods</h3>
-      <div id="method-M000002" class="method-detail">
-        <a name="M000002"></a>
-        <div class="method-heading">
-          <a href="#M000002" class="method-signature">
-          <span class="method-name">Generator.generate_script(my_exp_rest, t2_server, script_file) &rarr; nil<br />
-</span>
-          </a>
-        </div>
-        <div class="method-description">
-          <p>
-Generates the Galaxy tool&#8216;s script file responsible for talking to
-the taverna server
-</p>
-<dl>
-<dt><tt>my_exp_rest</tt></dt><dd>a <em>Workflow</em> object as returned from
-<em>MyExperimentREST.ReadWorkflow.new(url)</em>
-</dd>
-<dt><tt>t2_server</tt></dt><dd>a string containing the URL of the taverna 2 server
-</dd>
-<dt><tt>script_out</tt></dt><dd>the file handler to write the generated script code
-</dd>
-</dl>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000002-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000002-source">
-<pre>
-     <span class="ruby-comment cmt"># File lib/workflow-to-galaxy/generator.rb, line 490</span>
-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>)
-491:     <span class="ruby-identifier">script_preample</span>(<span class="ruby-identifier">script_out</span>)
-492:     <span class="ruby-identifier">script_util_methods</span>(<span class="ruby-identifier">script_out</span>)
-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>)
-494:     <span class="ruby-identifier">script_init_inputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
-495:     <span class="ruby-identifier">script_start_run</span>(<span class="ruby-identifier">script_out</span>)
-496:     <span class="ruby-identifier">script_get_outputs</span>(<span class="ruby-identifier">script_out</span>, <span class="ruby-identifier">t2_workflow</span>)
-497:     <span class="ruby-identifier">script_finish_run</span>(<span class="ruby-identifier">script_out</span>)
-498:   <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-      <div id="method-M000001" class="method-detail">
-        <a name="M000001"></a>
-        <div class="method-heading">
-          <a href="#M000001" class="method-signature">
-          <span class="method-name">Generator.generate_xml(my_exp_rest, xml_file) &rarr; nil<br />
-</span>
-          </a>
-        </div>
-        <div class="method-description">
-          <p>
-Generates the Galaxy tool&#8216;s xml file responsible for the UI.
-</p>
-<dl>
-<dt>+t2_workflow+</dt><dd>a <em>Workflow</em> object as returned from
-<em>MyExperimentREST::Workflows.new.read(url)</em>
-</dd>
-<dt><tt>xml_file</tt></dt><dd>a string containing the name of the generated XML file
-</dd>
-<dt><tt>xml_out</tt></dt><dd>the file handler to write the generated XML tags
-</dd>
-</dl>
-          <p><a class="source-toggle" href="#"
-            onclick="toggleCode('M000001-source');return false;">[Source]</a></p>
-          <div class="method-source-code" id="M000001-source">
-<pre>
-     <span class="ruby-comment cmt"># File lib/workflow-to-galaxy/generator.rb, line 471</span>
-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>)
-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>)
-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>))
-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>)
-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>)
-476:     <span class="ruby-identifier">help_tag</span>(<span class="ruby-identifier">xml_out</span>, <span class="ruby-identifier">t2_workflow</span>)
-477:     <span class="ruby-identifier">tool_end_tag</span>(<span class="ruby-identifier">xml_out</span>)
-478:   <span class="ruby-keyword kw">end</span>
-</pre>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-</body>
-</html>

data/doc/rdoc/classes/WorkflowToGalaxy.html DELETED Viewed

@@ -1,105 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>Module: WorkflowToGalaxy</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-    elemStyle = elem.style;
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-    return true;
-  }
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  // ]]>
-  </script>
-</head>
-<body>
-    <div id="classHeader">
-        <table class="header-table">
-        <tr class="top-aligned-row">
-          <td><strong>Module</strong></td>
-          <td class="class-name-in-header">WorkflowToGalaxy</td>
-        </tr>
-        <tr class="top-aligned-row">
-            <td><strong>In:</strong></td>
-            <td>
-                <a href="../files/lib/workflow-to-galaxy_rb.html">
-                lib/workflow-to-galaxy.rb
-                </a>
-        <br />
-            </td>
-        </tr>
-        </table>
-    </div>
-  <!-- banner header -->
-  <div id="bodyContent">
-  <div id="contextContent">
-   </div>
-  </div>
-    <!-- if includes -->
-    <div id="section">
-    <!-- if method_list -->
-  </div>
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-</body>
-</html>

data/doc/rdoc/files/LICENSE.html DELETED Viewed

@@ -1,133 +0,0 @@
-<?xml version="1.0" encoding="iso-8859-1"?>
-<!DOCTYPE html
-     PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-<head>
-  <title>File: LICENSE</title>
-  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-  <meta http-equiv="Content-Script-Type" content="text/javascript" />
-  <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
-  <script type="text/javascript">
-  // <![CDATA[
-  function popupCode( url ) {
-    window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
-  }
-  function toggleCode( id ) {
-    if ( document.getElementById )
-      elem = document.getElementById( id );
-    else if ( document.all )
-      elem = eval( "document.all." + id );
-    else
-      return false;
-    elemStyle = elem.style;
-    if ( elemStyle.display != "block" ) {
-      elemStyle.display = "block"
-    } else {
-      elemStyle.display = "none"
-    }
-    return true;
-  }
-  // Make codeblocks hidden by default
-  document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
-  // ]]>
-  </script>
-</head>
-<body>
-  <div id="fileHeader">
-    <h1>LICENSE</h1>
-    <table class="header-table">
-    <tr class="top-aligned-row">
-      <td><strong>Path:</strong></td>
-      <td>LICENSE
-      </td>
-    </tr>
-    <tr class="top-aligned-row">
-      <td><strong>Last Update:</strong></td>
-      <td>Wed Apr 06 16:41:53 +0200 2011</td>
-    </tr>
-    </table>
-  </div>
-  <!-- banner header -->
-  <div id="bodyContent">
-  <div id="contextContent">
-    <div id="description">
-      <h2>workflow-to-galaxy</h2>
-<p>
-The MIT License
-</p>
-<p>
-Copyright (c) 2010 - Netherlands Bioinformatics Centre
-</p>
-<p>
-Permission is hereby granted, free of charge, to any person obtaining a
-copy of this software and associated documentation files (the
-&quot;Software&quot;), to deal in the Software without restriction,
-including without limitation the rights to use, copy, modify, merge,
-publish, distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to the
-following conditions:
-</p>
-<p>
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-</p>
-<p>
-THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
-NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
-DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
-USE OR OTHER DEALINGS IN THE SOFTWARE.
-</p>
-    </div>
-   </div>
-  </div>
-    <!-- if includes -->
-    <div id="section">
-    <!-- if method_list -->
-  </div>
-<div id="validator-badges">
-  <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
-</div>
-</body>
-</html>