workflow-to-galaxy 0.3.4 → 0.3.5

Sign up to get free protection for your applications and to get access to all the features.
@@ -1,143 +1,171 @@
1
- <!DOCTYPE html>
2
-
3
- <html>
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
3
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
4
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
4
5
  <head>
5
- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
-
7
- <title>module WorkflowToGalaxy - workflow-to-galaxy Docs</title>
8
-
9
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
6
+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
10
7
 
11
- <script type="text/javascript">
12
- var rdoc_rel_prefix = "./";
13
- </script>
8
+ <title>Module: WorkflowToGalaxy</title>
14
9
 
15
- <script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
16
- <script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
17
- <script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
18
- <script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
19
- <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
20
- <script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
10
+ <link rel="stylesheet" href="./rdoc.css" type="text/css" media="screen" />
21
11
 
12
+ <script src="./js/jquery.js" type="text/javascript" charset="utf-8"></script>
13
+ <script src="./js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
14
+ <script src="./js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
15
+ <script src="./js/darkfish.js" type="text/javascript" charset="utf-8"></script>
22
16
 
17
+ </head>
23
18
  <body id="top" class="module">
24
- <nav id="metadata">
25
- <nav id="home-section" class="section">
26
- <h3 class="section-header">
27
- <a href="./index.html">Home</a>
28
- <a href="./table_of_contents.html#classes">Classes</a>
29
- <a href="./table_of_contents.html#methods">Methods</a>
30
- </h3>
31
- </nav>
32
-
33
-
34
- <nav id="search-section" class="section project-section" class="initially-hidden">
35
- <form action="#" method="get" accept-charset="utf-8">
36
- <h3 class="section-header">
37
- <input type="text" name="search" placeholder="Search" id="search-field"
38
- title="Type to search, Up and Down to navigate, Enter to load">
39
- </h3>
40
- </form>
41
-
42
- <ul id="search-results" class="initially-hidden"></ul>
43
- </nav>
44
-
45
-
46
- <div id="file-metadata">
47
- <nav id="file-list-section" class="section">
48
- <h3 class="section-header">Defined In</h3>
49
- <ul>
50
- <li>lib/workflow-to-galaxy.rb
51
- <li>lib/workflow-to-galaxy/galaxy.rb
52
- <li>lib/workflow-to-galaxy/constants.rb
53
- </ul>
54
- </nav>
55
19
 
56
-
20
+ <div id="metadata">
21
+ <div id="home-metadata">
22
+ <div id="home-section" class="section">
23
+ <h3 class="section-header">
24
+ <a href="./index.html">Home</a>
25
+ <a href="./index.html#classes">Classes</a>
26
+ <a href="./index.html#methods">Methods</a>
27
+ </h3>
28
+ </div>
29
+ </div>
30
+
31
+ <div id="file-metadata">
32
+ <div id="file-list-section" class="section">
33
+ <h3 class="section-header">In Files</h3>
34
+ <div class="section-body">
35
+ <ul>
36
+
37
+ <li><a href="./lib/workflow-to-galaxy_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
38
+ class="thickbox" title="lib/workflow-to-galaxy.rb">lib/workflow-to-galaxy.rb</a></li>
39
+
40
+ <li><a href="./lib/workflow-to-galaxy/constants_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
41
+ class="thickbox" title="lib/workflow-to-galaxy/constants.rb">lib/workflow-to-galaxy/constants.rb</a></li>
42
+
43
+ <li><a href="./lib/workflow-to-galaxy/galaxy_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
44
+ class="thickbox" title="lib/workflow-to-galaxy/galaxy.rb">lib/workflow-to-galaxy/galaxy.rb</a></li>
45
+
46
+ </ul>
47
+ </div>
48
+ </div>
49
+
50
+
51
+ </div>
52
+
53
+ <div id="class-metadata">
54
+
55
+
56
+
57
+
58
+
59
+ <!-- Namespace Contents -->
60
+ <div id="namespace-list-section" class="section">
61
+ <h3 class="section-header">Namespace</h3>
62
+ <ul class="link-list">
63
+
64
+ <li><span class="type">MODULE</span> <a href="WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
65
+
66
+ <li><span class="type">CLASS</span> <a href="WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
67
+
68
+ </ul>
69
+ </div>
70
+
71
+
72
+
73
+
74
+
75
+ <!-- Included Modules -->
76
+ <div id="includes-section" class="section">
77
+ <h3 class="section-header">Included Modules</h3>
78
+ <ul class="link-list">
79
+
80
+
81
+ <li><span class="include">MyExperimentREST</span></li>
82
+
83
+
84
+ </ul>
85
+ </div>
86
+
87
+ </div>
88
+
89
+ <div id="project-metadata">
90
+
91
+
92
+ <div id="fileindex-section" class="section project-section">
93
+ <h3 class="section-header">Files</h3>
94
+ <ul>
95
+
96
+ <li class="file"><a href="./CHANGES.html">CHANGES</a></li>
97
+
98
+ <li class="file"><a href="./LICENSE.html">LICENSE</a></li>
99
+
100
+ <li class="file"><a href="./README.html">README</a></li>
101
+
102
+ </ul>
103
+ </div>
104
+
105
+
106
+ <div id="classindex-section" class="section project-section">
107
+ <h3 class="section-header">Class/Module Index
108
+ <span class="search-toggle"><img src="./images/find.png"
109
+ height="16" width="16" alt="[+]"
110
+ title="show/hide quicksearch" /></span></h3>
111
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
112
+ <fieldset>
113
+ <legend>Quicksearch</legend>
114
+ <input type="text" name="quicksearch" value=""
115
+ class="quicksearch-field" />
116
+ </fieldset>
117
+ </form>
118
+
119
+ <ul class="link-list">
120
+
121
+ <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
122
+
123
+ <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
124
+
125
+ <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
126
+
127
+ <li><a href="./String.html">String</a></li>
128
+
129
+ </ul>
130
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
131
+ </div>
132
+
133
+
134
+ </div>
57
135
  </div>
58
136
 
59
- <div id="class-metadata">
60
-
61
-
62
- <!-- Included Modules -->
63
- <nav id="includes-section" class="section">
64
- <h3 class="section-header">Included Modules</h3>
137
+ <div id="documentation">
138
+ <h1 class="module">WorkflowToGalaxy</h1>
65
139
 
66
- <ul class="link-list">
67
-
68
-
69
- <li><span class="include">MyExperimentREST</span>
70
-
71
-
72
- </ul>
73
- </nav>
140
+ <div id="description" class="description">
141
+
142
+ </div><!-- description -->
74
143
 
75
144
 
76
- </div>
77
-
78
- <div id="project-metadata">
79
- <nav id="fileindex-section" class="section project-section">
80
- <h3 class="section-header">Pages</h3>
81
-
82
- <ul>
83
-
84
- <li class="file"><a href="./CHANGES.html">CHANGES</a>
85
-
86
- <li class="file"><a href="./LICENSE.html">LICENSE</a>
87
-
88
- <li class="file"><a href="./README.html">README</a>
89
-
90
- </ul>
91
- </nav>
92
-
93
- <nav id="classindex-section" class="section project-section">
94
- <h3 class="section-header">Class and Module Index</h3>
95
-
96
- <ul class="link-list">
97
-
98
- <li><a href="./WorkflowToGalaxy.html">WorkflowToGalaxy</a>
99
-
100
- <li><a href="./WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a>
101
-
102
- <li><a href="./WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a>
103
-
104
- <li><a href="./String.html">String</a>
105
-
106
- </ul>
107
- </nav>
108
-
109
- </div>
110
- </nav>
111
-
112
- <div id="documentation">
113
- <h1 class="module">module WorkflowToGalaxy</h1>
114
-
115
- <div id="description" class="description">
116
145
 
117
- </div><!-- description -->
118
-
119
-
120
-
121
-
122
- <section id="5Buntitled-5D" class="documentation-section">
123
146
 
147
+ <div id="5Buntitled-5D" class="documentation-section">
148
+
124
149
 
125
-
150
+
126
151
 
127
-
152
+
128
153
 
129
-
154
+
130
155
 
131
- <!-- Methods -->
132
-
133
- </section><!-- 5Buntitled-5D -->
156
+ <!-- Methods -->
157
+
158
+ </div><!-- 5Buntitled-5D -->
159
+
134
160
 
135
- </div><!-- documentation -->
161
+ </div><!-- documentation -->
136
162
 
163
+ <div id="validator-badges">
164
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
165
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
166
+ Rdoc Generator</a> 2</small>.</p>
167
+ </div>
137
168
 
138
- <footer id="validator-badges">
139
- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
140
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
141
- <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
142
- </footer>
169
+ </body>
170
+ </html>
143
171
 
@@ -1,245 +1,268 @@
1
- <!DOCTYPE html>
2
-
3
- <html>
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
3
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
4
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
4
5
  <head>
5
- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
-
7
- <title>class WorkflowToGalaxy::GalaxyTool - workflow-to-galaxy Docs</title>
6
+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type" />
8
7
 
9
- <link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
8
+ <title>Class: WorkflowToGalaxy::GalaxyTool</title>
10
9
 
11
- <script type="text/javascript">
12
- var rdoc_rel_prefix = "../";
13
- </script>
14
-
15
- <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
16
- <script type="text/javascript" charset="utf-8" src="../js/navigation.js"></script>
17
- <script type="text/javascript" charset="utf-8" src="../js/search_index.js"></script>
18
- <script type="text/javascript" charset="utf-8" src="../js/search.js"></script>
19
- <script type="text/javascript" charset="utf-8" src="../js/searcher.js"></script>
20
- <script type="text/javascript" charset="utf-8" src="../js/darkfish.js"></script>
10
+ <link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
21
11
 
12
+ <script src="../js/jquery.js" type="text/javascript" charset="utf-8"></script>
13
+ <script src="../js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
14
+ <script src="../js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
15
+ <script src="../js/darkfish.js" type="text/javascript" charset="utf-8"></script>
22
16
 
17
+ </head>
23
18
  <body id="top" class="class">
24
- <nav id="metadata">
25
- <nav id="home-section" class="section">
26
- <h3 class="section-header">
27
- <a href="../index.html">Home</a>
28
- <a href="../table_of_contents.html#classes">Classes</a>
29
- <a href="../table_of_contents.html#methods">Methods</a>
30
- </h3>
31
- </nav>
32
-
33
-
34
- <nav id="search-section" class="section project-section" class="initially-hidden">
35
- <form action="#" method="get" accept-charset="utf-8">
36
- <h3 class="section-header">
37
- <input type="text" name="search" placeholder="Search" id="search-field"
38
- title="Type to search, Up and Down to navigate, Enter to load">
39
- </h3>
40
- </form>
41
-
42
- <ul id="search-results" class="initially-hidden"></ul>
43
- </nav>
44
-
45
-
46
- <div id="file-metadata">
47
- <nav id="file-list-section" class="section">
48
- <h3 class="section-header">Defined In</h3>
49
- <ul>
50
- <li>lib/workflow-to-galaxy/galaxy.rb
51
- </ul>
52
- </nav>
53
19
 
54
-
55
- </div>
20
+ <div id="metadata">
21
+ <div id="home-metadata">
22
+ <div id="home-section" class="section">
23
+ <h3 class="section-header">
24
+ <a href="../index.html">Home</a>
25
+ <a href="../index.html#classes">Classes</a>
26
+ <a href="../index.html#methods">Methods</a>
27
+ </h3>
28
+ </div>
29
+ </div>
56
30
 
57
- <div id="class-metadata">
58
-
59
- <nav id="parent-class-section" class="section">
60
- <h3 class="section-header">Parent</h3>
61
-
62
- <p class="link">Object
63
-
64
- </nav>
31
+ <div id="file-metadata">
32
+ <div id="file-list-section" class="section">
33
+ <h3 class="section-header">In Files</h3>
34
+ <div class="section-body">
35
+ <ul>
36
+
37
+ <li><a href="../lib/workflow-to-galaxy/galaxy_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
38
+ class="thickbox" title="lib/workflow-to-galaxy/galaxy.rb">lib/workflow-to-galaxy/galaxy.rb</a></li>
39
+
40
+ </ul>
41
+ </div>
42
+ </div>
65
43
 
66
-
67
- <!-- Method Quickref -->
68
- <nav id="method-list-section" class="section">
69
- <h3 class="section-header">Methods</h3>
44
+
45
+ </div>
70
46
 
71
- <ul class="link-list">
72
-
73
- <li><a href="#method-c-new">::new</a>
74
-
75
- <li><a href="#method-i-generate">#generate</a>
76
-
77
- </ul>
78
- </nav>
47
+ <div id="class-metadata">
48
+
49
+ <!-- Parent Class -->
50
+ <div id="parent-class-section" class="section">
51
+ <h3 class="section-header">Parent</h3>
52
+
53
+ <p class="link">Object</p>
54
+
55
+ </div>
56
+
79
57
 
80
- </div>
58
+
81
59
 
82
- <div id="project-metadata">
83
- <nav id="fileindex-section" class="section project-section">
84
- <h3 class="section-header">Pages</h3>
60
+
85
61
 
86
- <ul>
87
-
88
- <li class="file"><a href="../CHANGES.html">CHANGES</a>
89
-
90
- <li class="file"><a href="../LICENSE.html">LICENSE</a>
91
-
92
- <li class="file"><a href="../README.html">README</a>
93
-
94
- </ul>
95
- </nav>
62
+
63
+ <!-- Method Quickref -->
64
+ <div id="method-list-section" class="section">
65
+ <h3 class="section-header">Methods</h3>
66
+ <ul class="link-list">
67
+
68
+ <li><a href="#method-c-new">::new</a></li>
69
+
70
+ <li><a href="#method-i-generate">#generate</a></li>
71
+
72
+ </ul>
73
+ </div>
74
+
96
75
 
97
- <nav id="classindex-section" class="section project-section">
98
- <h3 class="section-header">Class and Module Index</h3>
76
+
77
+ </div>
99
78
 
100
- <ul class="link-list">
101
-
102
- <li><a href="../WorkflowToGalaxy.html">WorkflowToGalaxy</a>
103
-
104
- <li><a href="../WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a>
105
-
106
- <li><a href="../WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a>
107
-
108
- <li><a href="../String.html">String</a>
109
-
110
- </ul>
111
- </nav>
79
+ <div id="project-metadata">
80
+
81
+
82
+ <div id="fileindex-section" class="section project-section">
83
+ <h3 class="section-header">Files</h3>
84
+ <ul>
85
+
86
+ <li class="file"><a href="../CHANGES.html">CHANGES</a></li>
87
+
88
+ <li class="file"><a href="../LICENSE.html">LICENSE</a></li>
89
+
90
+ <li class="file"><a href="../README.html">README</a></li>
91
+
92
+ </ul>
93
+ </div>
94
+
95
+
96
+ <div id="classindex-section" class="section project-section">
97
+ <h3 class="section-header">Class/Module Index
98
+ <span class="search-toggle"><img src="../images/find.png"
99
+ height="16" width="16" alt="[+]"
100
+ title="show/hide quicksearch" /></span></h3>
101
+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
102
+ <fieldset>
103
+ <legend>Quicksearch</legend>
104
+ <input type="text" name="quicksearch" value=""
105
+ class="quicksearch-field" />
106
+ </fieldset>
107
+ </form>
108
+
109
+ <ul class="link-list">
110
+
111
+ <li><a href="../WorkflowToGalaxy.html">WorkflowToGalaxy</a></li>
112
+
113
+ <li><a href="../WorkflowToGalaxy/GalaxyTool.html">WorkflowToGalaxy::GalaxyTool</a></li>
114
+
115
+ <li><a href="../WorkflowToGalaxy/Workflows.html">WorkflowToGalaxy::Workflows</a></li>
116
+
117
+ <li><a href="../String.html">String</a></li>
118
+
119
+ </ul>
120
+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
121
+ </div>
112
122
 
123
+
124
+ </div>
113
125
  </div>
114
- </nav>
115
126
 
116
- <div id="documentation">
117
- <h1 class="class">class WorkflowToGalaxy::GalaxyTool</h1>
127
+ <div id="documentation">
128
+ <h1 class="class">WorkflowToGalaxy::GalaxyTool</h1>
118
129
 
119
- <div id="description" class="description">
120
-
130
+ <div id="description" class="description">
131
+
121
132
  <p>The <em><a href="GalaxyTool.html">GalaxyTool</a></em> class contains a
122
- <code>generate</code> public method that generates the required files (XML
123
- and script) for a Galaxy tool.</p>
133
+ <tt>generate</tt> public method that generates the required files (XML and
134
+ script) for a Galaxy tool.</p>
124
135
 
125
- </div><!-- description -->
136
+ </div><!-- description -->
126
137
 
127
-
128
-
129
-
130
- <section id="5Buntitled-5D" class="documentation-section">
131
138
 
132
-
133
139
 
134
-
135
140
 
141
+ <div id="5Buntitled-5D" class="documentation-section">
142
+
136
143
 
137
-
138
- <!-- Attributes -->
139
- <section id="attribute-method-details" class="method-section section">
140
- <h3 class="section-header">Attributes</h3>
144
+
141
145
 
142
146
 
143
- <div id="attribute-i-config" class="method-detail">
144
- <div class="method-heading attribute-method-heading">
145
- <span class="method-name">config</span><span
146
- class="attribute-access-type">[RW]</span>
147
- </div>
148
147
 
149
- <div class="method-description">
150
-
151
- <p><code>config</code> contains data needed in relation to what the tool will
152
- do and <code>wkf_object</code> contains the workflow object that will be
153
- used to generate the galaxy tool</p>
154
-
155
- </div>
156
- </div>
157
148
 
158
- <div id="attribute-i-wkf_object" class="method-detail">
159
- <div class="method-heading attribute-method-heading">
160
- <span class="method-name">wkf_object</span><span
161
- class="attribute-access-type">[RW]</span>
162
- </div>
149
+ <!-- Attributes -->
150
+ <div id="attribute-method-details" class="method-section section">
151
+ <h3 class="section-header">Attributes</h3>
163
152
 
164
- <div class="method-description">
165
153
 
166
- <p><code>config</code> contains data needed in relation to what the tool will
167
- do and <code>wkf_object</code> contains the workflow object that will be
168
- used to generate the galaxy tool</p>
154
+ <div id="config-attribute-method" class="method-detail">
155
+ <a name="config"></a>
156
+
157
+ <a name="config="></a>
158
+
159
+ <div class="method-heading attribute-method-heading">
160
+ <span class="method-name">config</span><span
161
+ class="attribute-access-type">[RW]</span>
162
+ </div>
163
+
164
+ <div class="method-description">
165
+
166
+ <p><tt>config</tt> contains data needed in relation to what the tool will do
167
+ and <tt>wkf_object</tt> contains the workflow object that will be used to
168
+ generate the galaxy tool</p>
169
+
170
+ </div>
171
+ </div>
169
172
 
173
+ <div id="wkf_object-attribute-method" class="method-detail">
174
+ <a name="wkf_object"></a>
175
+
176
+ <a name="wkf_object="></a>
177
+
178
+ <div class="method-heading attribute-method-heading">
179
+ <span class="method-name">wkf_object</span><span
180
+ class="attribute-access-type">[RW]</span>
181
+ </div>
182
+
183
+ <div class="method-description">
184
+
185
+ <p><tt>config</tt> contains data needed in relation to what the tool will do
186
+ and <tt>wkf_object</tt> contains the workflow object that will be used to
187
+ generate the galaxy tool</p>
188
+
189
+ </div>
170
190
  </div>
171
- </div>
191
+
192
+ </div><!-- attribute-method-details -->
172
193
 
173
- </section><!-- attribute-method-details -->
174
-
175
194
 
176
- <!-- Methods -->
177
-
178
- <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
179
- <h3 class="section-header">Public Class Methods</h3>
195
+ <!-- Methods -->
196
+
197
+ <div id="public-class-method-details" class="method-section section">
198
+ <h3 class="section-header">Public Class Methods</h3>
180
199
 
181
-
182
- <div id="method-c-new" class="method-detail ">
183
-
184
- <div class="method-heading">
185
- <span class="method-name">new</span><span
186
- class="method-args">(config)</span>
187
- <span class="method-click-advice">click to toggle source</span>
188
- </div>
189
-
200
+
201
+ <div id="new-method" class="method-detail ">
202
+ <a name="method-c-new"></a>
190
203
 
191
- <div class="method-description">
192
204
 
193
- <p>-</p>
205
+ <div class="method-heading">
206
+ <span class="method-name">new</span><span
207
+ class="method-args">(config)</span>
208
+ <span class="method-click-advice">click to toggle source</span>
209
+ </div>
210
+
211
+
212
+ <div class="method-description">
213
+
214
+ <p>-</p>
194
215
 
195
216
  <pre>TODO: does initialize appear in rdoc? -- these will go to README as well...</pre>
196
-
217
+
197
218
 
198
-
199
- <div class="method-source-code" id="new-source">
200
- <pre><span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 40</span>
219
+
220
+ <div class="method-source-code" id="new-source">
221
+ <pre>
222
+ <span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 40</span>
201
223
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">config</span>)
202
224
  <span class="ruby-ivar">@config</span> = <span class="ruby-identifier">config</span>
203
225
  <span class="ruby-keyword">end</span></pre>
204
- </div><!-- new-source -->
205
-
206
- </div>
226
+ </div><!-- new-source -->
227
+
228
+ </div>
207
229
 
208
-
230
+
209
231
 
210
-
211
- </div><!-- new-method -->
232
+
233
+ </div><!-- new-method -->
212
234
 
235
+
236
+ </div><!-- public-class-method-details -->
213
237
 
214
- </section><!-- public-class-method-details -->
215
-
216
- <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
217
- <h3 class="section-header">Public Instance Methods</h3>
238
+ <div id="public-instance-method-details" class="method-section section">
239
+ <h3 class="section-header">Public Instance Methods</h3>
240
+
241
+
242
+ <div id="generate-method" class="method-detail ">
243
+ <a name="method-i-generate"></a>
218
244
 
219
-
220
- <div id="method-i-generate" class="method-detail ">
221
-
222
-
223
- <div class="method-heading">
224
- <span class="method-callseq">
225
- generate() &rarr; nil
226
- </span>
227
245
 
228
- <span class="method-click-advice">click to toggle source</span>
229
246
 
230
- </div>
231
-
232
-
233
-
234
- <div class="method-description">
247
+ <div class="method-heading">
248
+ <span class="method-callseq">generate() &rarr; nil</span>
249
+
250
+ <span class="method-click-advice">click to toggle source</span>
251
+
252
+ </div>
235
253
 
236
- <p>Generates the two files needed for a Galaxy tool: a configuration file
237
- (XML) and a processing file (in our case a ruby script)</p>
238
254
 
239
255
 
240
-
241
- <div class="method-source-code" id="generate-source">
242
- <pre><span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 582</span>
256
+ <div class="method-description">
257
+
258
+ <p>Generates the two files needed for a Galaxy tool: a configuration file
259
+ (XML) and a processing file (in our case a ruby script)</p>
260
+
261
+
262
+
263
+ <div class="method-source-code" id="generate-source">
264
+ <pre>
265
+ <span class="ruby-comment"># File lib/workflow-to-galaxy/galaxy.rb, line 582</span>
243
266
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">generate</span>
244
267
 
245
268
  <span class="ruby-keyword">if</span>(<span class="ruby-identifier">config</span>[<span class="ruby-value">:params</span>][<span class="ruby-value">:response</span>])
@@ -296,26 +319,29 @@ used to generate the galaxy tool</p>
296
319
 
297
320
 
298
321
  <span class="ruby-keyword">end</span></pre>
299
- </div><!-- generate-source -->
300
-
301
- </div>
322
+ </div><!-- generate-source -->
323
+
324
+ </div>
302
325
 
303
-
326
+
304
327
 
305
-
306
- </div><!-- generate-method -->
328
+
329
+ </div><!-- generate-method -->
307
330
 
331
+
332
+ </div><!-- public-instance-method-details -->
308
333
 
309
- </section><!-- public-instance-method-details -->
334
+ </div><!-- 5Buntitled-5D -->
310
335
 
311
- </section><!-- 5Buntitled-5D -->
312
336
 
313
- </div><!-- documentation -->
337
+ </div><!-- documentation -->
314
338
 
339
+ <div id="validator-badges">
340
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
341
+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
342
+ Rdoc Generator</a> 2</small>.</p>
343
+ </div>
315
344
 
316
- <footer id="validator-badges">
317
- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
318
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
319
- <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
320
- </footer>
345
+ </body>
346
+ </html>
321
347