workflow-to-galaxy 0.2.7 → 0.2.8

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Files changed (48) hide show
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  2. data/README +11 -10
  3. data/Rakefile +7 -6
  4. data/doc/rdoc/CHANGES.html +105 -0
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  7. data/doc/rdoc/README.html +167 -0
  8. data/doc/rdoc/WorkflowToGalaxy.html +135 -0
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  35. data/doc/rdoc/lib/workflow-to-galaxy/generator_rb.html +55 -0
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  38. metadata +52 -14
  39. data/doc/rdoc/classes/Generator.html +0 -215
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  41. data/doc/rdoc/files/LICENSE.html +0 -133
  42. data/doc/rdoc/files/README.html +0 -192
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- <td><strong>Path:</strong></td>
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- <td>README
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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>Thu Jul 21 18:53:40 +0200 2011</td>
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- </tr>
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- </table>
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- </div>
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- <!-- banner header -->
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- <h1>workflow-to-galaxy tool generator</h1>
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- <table>
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- <tr><td valign="top">Authors:</td><td>Konstantinos Karasavvas
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-
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- </td></tr>
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- <tr><td valign="top">Gem Version:</td><td>0.2.7
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-
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- </td></tr>
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- <tr><td valign="top">Contact:</td><td><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a>
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-
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- </td></tr>
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- <tr><td valign="top">Licence:</td><td>MIT (See LICENCE or <a
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- href="http://www.opensource.org/licenses/mit-license">www.opensource.org/licenses/mit-license</a>)
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-
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- </td></tr>
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- <tr><td valign="top">Copyright:</td><td>(c) 2010 Netherlands Bioinformatics Centre, The Netherlands
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-
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- </td></tr>
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- </table>
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- <h2>Synopsis</h2>
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- <p>
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- This script requires a Taverna2 workflow URL as input and generates a
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- Galaxy tool (a UI XML definition plus a script) that will enable the
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- execution of this workflow through Galaxy. The tool&#8216;s description is
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- as good as the description provided in the workflow itself. Currently, the
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- myExperiment workflow repository is used to access workflow information via
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- its REST API but a workflow description from a file is also supported.
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- </p>
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- <p>
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- The name is workflow-to-galaxy rather than t2-workflow-to-galaxy because it
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- is possible that it will support other workflow management system&#8216;s
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- in the future.
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- </p>
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- <h2>Installation</h2>
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- <dl>
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- <dt>sudo</dt><dd>gem install workflow-to-galaxy
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-
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- </dd>
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- </dl>
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- <h2>Usage</h2>
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- <p>
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- workflow_to_galaxy [options] &lt;myExperiement-workflow&gt; |
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- &lt;t2flow-file&gt;
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- </p>
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- <p>
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- Generates a Galaxy tool (a UI xml definition plus a script) for the
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- specified Taverna2 workflow, where &lt;myExperiment-workflow&gt; is the
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- full URL of the workflow in the myExperiment website. Alternatively a
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- t2flow file can be passed for workflows not in myExperiment. Available
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- options are:
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- </p>
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- <p>
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- -o OUTPUT, &#8212;output=OUTPUT The file name(s) of the generated tool. If
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- it is not specified then the workflow&#8216;s name will be used.
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- </p>
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- <p>
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- -s SERVER, &#8212;server=SERVER The taverna server that the script will
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- request execution from. If it is not specified then &quot;<a
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- href="http://localhost:8980/taverna-server">localhost:8980/taverna-server</a>&quot;
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- will be used.
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- </p>
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- <p>
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- -t, &#8212;t2flow The workflow is a t2flow file.
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- </p>
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- <h2>Example</h2>
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- <p>
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- Let&#8216;s say we want to install the taverna2 workflow <a
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- href="http://www.myexperiment.org/workflows/74.html">www.myexperiment.org/workflows/74.html</a>
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- from myExperiment repository:
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- </p>
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- <p>
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- <tt>$ workflow_to_galaxy -s <a
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- href="http://localhost:8980/taverna-server">localhost:8980/taverna-server</a>
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- <a
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- href="http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5">www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_781733.t2flow?version=5</a></tt>
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- </p>
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- <h2>References</h2>
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- <table>
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- <tr><td valign="top">Galaxy:</td><td><a href="http://galaxy.psu.edu">galaxy.psu.edu</a>
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-
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- </td></tr>
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- <tr><td valign="top">Taverna2:</td><td><a href="http://www.taverna.org.uk">www.taverna.org.uk</a>
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-
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- </td></tr>
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- <tr><td valign="top">myExperiment:</td><td><a href="http://www.myexperiment.org">www.myexperiment.org</a>
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- </td></tr>
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- </table>
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- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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- <td>Mon Jul 04 16:13:08 +0200 2011</td>
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- The <a href="../../../classes/Generator.html">Generator</a> module contains
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- <td>lib/workflow-to-galaxy.rb
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- </td>
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- </tr>
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- <td><strong>Last Update:</strong></td>
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- <td>Mon Dec 13 15:22:40 +0100 2010</td>
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- workflow-to-galaxy/generator&nbsp;&nbsp;
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- h1 { font-size: 150%; }
13
- h2,h3,h4 { margin-top: 1em; }
14
-
15
- a { background: #eef; color: #039; text-decoration: none; }
16
- a:hover { background: #039; color: #eef; }
17
-
18
- /* Override the base stylesheet's Anchor inside a table cell */
19
- td > a {
20
- background: transparent;
21
- color: #039;
22
- text-decoration: none;
23
- }
24
-
25
- /* and inside a section title */
26
- .section-title > a {
27
- background: transparent;
28
- color: #eee;
29
- text-decoration: none;
30
- }
31
-
32
- /* === Structural elements =================================== */
33
-
34
- div#index {
35
- margin: 0;
36
- margin-left: -40px;
37
- padding: 0;
38
- font-size: 90%;
39
- }
40
-
41
-
42
- div#index a {
43
- margin-left: 0.7em;
44
- }
45
-
46
- div#index .section-bar {
47
- margin-left: 0px;
48
- padding-left: 0.7em;
49
- background: #ccc;
50
- font-size: small;
51
- }
52
-
53
-
54
- div#classHeader, div#fileHeader {
55
- width: auto;
56
- color: white;
57
- padding: 0.5em 1.5em 0.5em 1.5em;
58
- margin: 0;
59
- margin-left: -40px;
60
- border-bottom: 3px solid #006;
61
- }
62
-
63
- div#classHeader a, div#fileHeader a {
64
- background: inherit;
65
- color: white;
66
- }
67
-
68
- div#classHeader td, div#fileHeader td {
69
- background: inherit;
70
- color: white;
71
- }
72
-
73
-
74
- div#fileHeader {
75
- background: #057;
76
- }
77
-
78
- div#classHeader {
79
- background: #048;
80
- }
81
-
82
-
83
- .class-name-in-header {
84
- font-size: 180%;
85
- font-weight: bold;
86
- }
87
-
88
-
89
- div#bodyContent {
90
- padding: 0 1.5em 0 1.5em;
91
- }
92
-
93
- div#description {
94
- padding: 0.5em 1.5em;
95
- background: #efefef;
96
- border: 1px dotted #999;
97
- }
98
-
99
- div#description h1,h2,h3,h4,h5,h6 {
100
- color: #125;;
101
- background: transparent;
102
- }
103
-
104
- div#validator-badges {
105
- text-align: center;
106
- }
107
- div#validator-badges img { border: 0; }
108
-
109
- div#copyright {
110
- color: #333;
111
- background: #efefef;
112
- font: 0.75em sans-serif;
113
- margin-top: 5em;
114
- margin-bottom: 0;
115
- padding: 0.5em 2em;
116
- }
117
-
118
-
119
- /* === Classes =================================== */
120
-
121
- table.header-table {
122
- color: white;
123
- font-size: small;
124
- }
125
-
126
- .type-note {
127
- font-size: small;
128
- color: #DEDEDE;
129
- }
130
-
131
- .xxsection-bar {
132
- background: #eee;
133
- color: #333;
134
- padding: 3px;
135
- }
136
-
137
- .section-bar {
138
- color: #333;
139
- border-bottom: 1px solid #999;
140
- margin-left: -20px;
141
- }
142
-
143
-
144
- .section-title {
145
- background: #79a;
146
- color: #eee;
147
- padding: 3px;
148
- margin-top: 2em;
149
- margin-left: -30px;
150
- border: 1px solid #999;
151
- }
152
-
153
- .top-aligned-row { vertical-align: top }
154
- .bottom-aligned-row { vertical-align: bottom }
155
-
156
- /* --- Context section classes ----------------------- */
157
-
158
- .context-row { }
159
- .context-item-name { font-family: monospace; font-weight: bold; color: black; }
160
- .context-item-value { font-size: small; color: #448; }
161
- .context-item-desc { color: #333; padding-left: 2em; }
162
-
163
- /* --- Method classes -------------------------- */
164
- .method-detail {
165
- background: #efefef;
166
- padding: 0;
167
- margin-top: 0.5em;
168
- margin-bottom: 1em;
169
- border: 1px dotted #ccc;
170
- }
171
- .method-heading {
172
- color: black;
173
- background: #ccc;
174
- border-bottom: 1px solid #666;
175
- padding: 0.2em 0.5em 0 0.5em;
176
- }
177
- .method-signature { color: black; background: inherit; }
178
- .method-name { font-weight: bold; }
179
- .method-args { font-style: italic; }
180
- .method-description { padding: 0 0.5em 0 0.5em; }
181
-
182
- /* --- Source code sections -------------------- */
183
-
184
- a.source-toggle { font-size: 90%; }
185
- div.method-source-code {
186
- background: #262626;
187
- color: #ffdead;
188
- margin: 1em;
189
- padding: 0.5em;
190
- border: 1px dashed #999;
191
- overflow: hidden;
192
- }
193
-
194
- div.method-source-code pre { color: #ffdead; overflow: hidden; }
195
-
196
- /* --- Ruby keyword styles --------------------- */
197
-
198
- .standalone-code { background: #221111; color: #ffdead; overflow: hidden; }
199
-
200
- .ruby-constant { color: #7fffd4; background: transparent; }
201
- .ruby-keyword { color: #00ffff; background: transparent; }
202
- .ruby-ivar { color: #eedd82; background: transparent; }
203
- .ruby-operator { color: #00ffee; background: transparent; }
204
- .ruby-identifier { color: #ffdead; background: transparent; }
205
- .ruby-node { color: #ffa07a; background: transparent; }
206
- .ruby-comment { color: #b22222; font-weight: bold; background: transparent; }
207
- .ruby-regexp { color: #ffa07a; background: transparent; }
208
- .ruby-value { color: #7fffd4; background: transparent; }