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.
- data/Rakefile +2 -2
- data/doc/rdoc/CHANGES.html +92 -89
- data/doc/rdoc/LICENSE.html +91 -89
- data/doc/rdoc/README.html +110 -107
- data/doc/rdoc/String.html +163 -148
- data/doc/rdoc/WorkflowToGalaxy.html +149 -121
- data/doc/rdoc/WorkflowToGalaxy/GalaxyTool.html +227 -201
- data/doc/rdoc/WorkflowToGalaxy/Workflows.html +127 -115
- data/doc/rdoc/created.rid +7 -7
- data/doc/rdoc/index.html +87 -104
- data/doc/rdoc/js/darkfish.js +62 -99
- data/doc/rdoc/js/jquery.js +29 -15
- data/doc/rdoc/rdoc.css +339 -119
- metadata +101 -116
@@ -1,143 +1,171 @@
|
|
1
|
-
|
2
|
-
|
3
|
-
|
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
|
-
<
|
12
|
-
var rdoc_rel_prefix = "./";
|
13
|
-
</script>
|
8
|
+
<title>Module: WorkflowToGalaxy</title>
|
14
9
|
|
15
|
-
<
|
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&height=550&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&height=550&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&height=550&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="
|
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
|
-
|
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
|
-
|
132
|
-
|
133
|
-
|
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
|
-
|
139
|
-
|
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
|
-
|
2
|
-
|
3
|
-
|
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
|
-
<
|
8
|
+
<title>Class: WorkflowToGalaxy::GalaxyTool</title>
|
10
9
|
|
11
|
-
<
|
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
|
-
|
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
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
</
|
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&height=550&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
|
-
|
68
|
-
<nav id="method-list-section" class="section">
|
69
|
-
<h3 class="section-header">Methods</h3>
|
44
|
+
|
45
|
+
</div>
|
70
46
|
|
71
|
-
|
72
|
-
|
73
|
-
|
74
|
-
|
75
|
-
|
76
|
-
|
77
|
-
|
78
|
-
|
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
|
-
|
58
|
+
|
81
59
|
|
82
|
-
|
83
|
-
<nav id="fileindex-section" class="section project-section">
|
84
|
-
<h3 class="section-header">Pages</h3>
|
60
|
+
|
85
61
|
|
86
|
-
|
87
|
-
|
88
|
-
|
89
|
-
|
90
|
-
|
91
|
-
|
92
|
-
|
93
|
-
|
94
|
-
|
95
|
-
|
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
|
-
|
98
|
-
|
76
|
+
|
77
|
+
</div>
|
99
78
|
|
100
|
-
|
101
|
-
|
102
|
-
|
103
|
-
|
104
|
-
|
105
|
-
|
106
|
-
|
107
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
</
|
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
|
-
|
127
|
+
<div id="documentation">
|
128
|
+
<h1 class="class">WorkflowToGalaxy::GalaxyTool</h1>
|
118
129
|
|
119
|
-
|
120
|
-
|
130
|
+
<div id="description" class="description">
|
131
|
+
|
121
132
|
<p>The <em><a href="GalaxyTool.html">GalaxyTool</a></em> class contains a
|
122
|
-
<
|
123
|
-
|
133
|
+
<tt>generate</tt> public method that generates the required files (XML and
|
134
|
+
script) for a Galaxy tool.</p>
|
124
135
|
|
125
|
-
|
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
|
-
|
159
|
-
|
160
|
-
|
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
|
-
<
|
167
|
-
|
168
|
-
|
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
|
-
|
191
|
+
|
192
|
+
</div><!-- attribute-method-details -->
|
172
193
|
|
173
|
-
</section><!-- attribute-method-details -->
|
174
|
-
|
175
194
|
|
176
|
-
|
177
|
-
|
178
|
-
|
179
|
-
|
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
|
-
|
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
|
-
<
|
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
|
-
|
200
|
-
|
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
|
-
|
205
|
-
|
206
|
-
|
226
|
+
</div><!-- new-source -->
|
227
|
+
|
228
|
+
</div>
|
207
229
|
|
208
|
-
|
230
|
+
|
209
231
|
|
210
|
-
|
211
|
-
|
232
|
+
|
233
|
+
</div><!-- new-method -->
|
212
234
|
|
235
|
+
|
236
|
+
</div><!-- public-class-method-details -->
|
213
237
|
|
214
|
-
|
215
|
-
|
216
|
-
|
217
|
-
|
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() → nil
|
226
|
-
</span>
|
227
245
|
|
228
|
-
<span class="method-click-advice">click to toggle source</span>
|
229
246
|
|
230
|
-
|
231
|
-
|
232
|
-
|
233
|
-
|
234
|
-
|
247
|
+
<div class="method-heading">
|
248
|
+
<span class="method-callseq">generate() → 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
|
-
|
242
|
-
<
|
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
|
-
|
300
|
-
|
301
|
-
|
322
|
+
</div><!-- generate-source -->
|
323
|
+
|
324
|
+
</div>
|
302
325
|
|
303
|
-
|
326
|
+
|
304
327
|
|
305
|
-
|
306
|
-
|
328
|
+
|
329
|
+
</div><!-- generate-method -->
|
307
330
|
|
331
|
+
|
332
|
+
</div><!-- public-instance-method-details -->
|
308
333
|
|
309
|
-
</
|
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
|
-
|
317
|
-
|
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
|
|