|
7
|
1
|
|
|
2
|
|
|
3
|
|
|
4 <!DOCTYPE html>
|
|
|
5 <html lang="en" class="">
|
|
|
6 <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#">
|
|
|
7 <meta charset='utf-8'>
|
|
|
8 <meta http-equiv="X-UA-Compatible" content="IE=edge">
|
|
|
9 <meta http-equiv="Content-Language" content="en">
|
|
|
10
|
|
|
11
|
|
|
12 <title>vipints/GFFtools-GX ยท GitHub</title>
|
|
|
13 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
|
|
|
14 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
|
|
|
15 <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png">
|
|
|
16 <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png">
|
|
|
17 <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png">
|
|
|
18 <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144.png">
|
|
|
19 <meta property="fb:app_id" content="1401488693436528">
|
|
|
20
|
|
|
21 <meta content="@github" name="twitter:site" /><meta content="summary" name="twitter:card" /><meta content="vipints/GFFtools-GX" name="twitter:title" /><meta content="GFFtools-GX - gfftools - Galaxy toolshed repository" name="twitter:description" /><meta content="https://avatars3.githubusercontent.com/u/1714549?v=3&s=400" name="twitter:image:src" />
|
|
|
22 <meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars3.githubusercontent.com/u/1714549?v=3&s=400" property="og:image" /><meta content="vipints/GFFtools-GX" property="og:title" /><meta content="https://github.com/vipints/GFFtools-GX" property="og:url" /><meta content="GFFtools-GX - gfftools - Galaxy toolshed repository" property="og:description" />
|
|
|
23 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
|
|
|
24 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
|
|
|
25 <link rel="assets" href="https://assets-cdn.github.com/">
|
|
|
26
|
|
|
27 <meta name="pjax-timeout" content="1000">
|
|
|
28
|
|
|
29
|
|
|
30 <meta name="msapplication-TileImage" content="/windows-tile.png">
|
|
|
31 <meta name="msapplication-TileColor" content="#ffffff">
|
|
|
32 <meta name="selected-link" value="repo_source" data-pjax-transient>
|
|
|
33 <meta name="google-analytics" content="UA-3769691-2">
|
|
|
34
|
|
|
35 <meta content="collector.githubapp.com" name="octolytics-host" /><meta content="collector-cdn.github.com" name="octolytics-script-host" /><meta content="github" name="octolytics-app-id" /><meta content="8076FA05:70D4:60A61D0:5539676F" name="octolytics-dimension-request_id" />
|
|
|
36
|
|
|
37 <meta content="Rails, view, files#disambiguate" name="analytics-event" />
|
|
|
38 <meta class="js-ga-set" name="dimension1" content="Logged Out">
|
|
|
39 <meta class="js-ga-set" name="dimension2" content="Header v3">
|
|
|
40 <meta name="is-dotcom" content="true">
|
|
|
41 <meta name="hostname" content="github.com">
|
|
|
42 <meta name="user-login" content="">
|
|
|
43
|
|
|
44
|
|
|
45 <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico">
|
|
|
46
|
|
|
47
|
|
|
48 <meta content="authenticity_token" name="csrf-param" />
|
|
|
49 <meta content="q2DwFmudId8h0AkXoplSINROJqJv7BQJZx3Y7Hs/VPrrrSaNAsWynI2E/KP2zj0WsGxL5x85Jq9uwj3l7rLpFg==" name="csrf-token" />
|
|
|
50
|
|
|
51 <link href="https://assets-cdn.github.com/assets/github-fbb88baa8c28184f25d1a972d401bb2e63fbed64378a172707460803c12c0440.css" media="all" rel="stylesheet" />
|
|
|
52 <link href="https://assets-cdn.github.com/assets/github2-b11477f9aa851e67e46efbb84c8c2c776615ebb9fb07c4551873a066c4e48f67.css" media="all" rel="stylesheet" />
|
|
|
53
|
|
|
54
|
|
|
55
|
|
|
56
|
|
|
57 <meta http-equiv="x-pjax-version" content="dd45ac9a07a24b9779f43a888c4447e3">
|
|
|
58
|
|
|
59
|
|
|
60 <meta name="description" content="GFFtools-GX - gfftools - Galaxy toolshed repository">
|
|
|
61 <meta name="go-import" content="github.com/vipints/GFFtools-GX git https://github.com/vipints/GFFtools-GX.git">
|
|
|
62
|
|
|
63 <meta content="1714549" name="octolytics-dimension-user_id" /><meta content="vipints" name="octolytics-dimension-user_login" /><meta content="19711908" name="octolytics-dimension-repository_id" /><meta content="vipints/GFFtools-GX" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="19711908" name="octolytics-dimension-repository_network_root_id" /><meta content="vipints/GFFtools-GX" name="octolytics-dimension-repository_network_root_nwo" />
|
|
|
64 <link href="https://github.com/vipints/GFFtools-GX/commits/master.atom" rel="alternate" title="Recent Commits to GFFtools-GX:master" type="application/atom+xml">
|
|
|
65
|
|
|
66 </head>
|
|
|
67
|
|
|
68
|
|
|
69 <body class="logged_out env-production vis-public">
|
|
|
70 <a href="#start-of-content" tabindex="1" class="accessibility-aid js-skip-to-content">Skip to content</a>
|
|
|
71 <div class="wrapper">
|
|
|
72
|
|
|
73
|
|
|
74
|
|
|
75
|
|
|
76
|
|
|
77
|
|
|
78 <div class="header header-logged-out" role="banner">
|
|
|
79 <div class="container clearfix">
|
|
|
80
|
|
|
81 <a class="header-logo-wordmark" href="https://github.com/" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
|
|
|
82 <span class="mega-octicon octicon-logo-github"></span>
|
|
|
83 </a>
|
|
|
84
|
|
|
85 <div class="header-actions" role="navigation">
|
|
|
86 <a class="btn btn-primary" href="/join" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a>
|
|
|
87 <a class="btn" href="/login?return_to=%2Fvipints%2FGFFtools-GX" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a>
|
|
|
88 </div>
|
|
|
89
|
|
|
90 <div class="site-search repo-scope js-site-search" role="search">
|
|
|
91 <form accept-charset="UTF-8" action="/vipints/GFFtools-GX/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/vipints/GFFtools-GX/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div>
|
|
|
92 <input type="text"
|
|
|
93 class="js-site-search-field is-clearable"
|
|
|
94 data-hotkey="s"
|
|
|
95 name="q"
|
|
|
96 placeholder="Search"
|
|
|
97 data-global-scope-placeholder="Search GitHub"
|
|
|
98 data-repo-scope-placeholder="Search"
|
|
|
99 tabindex="1"
|
|
|
100 autocapitalize="off">
|
|
|
101 <div class="scope-badge">This repository</div>
|
|
|
102 </form>
|
|
|
103 </div>
|
|
|
104
|
|
|
105 <ul class="header-nav left" role="navigation">
|
|
|
106 <li class="header-nav-item">
|
|
|
107 <a class="header-nav-link" href="/explore" data-ga-click="(Logged out) Header, go to explore, text:explore">Explore</a>
|
|
|
108 </li>
|
|
|
109 <li class="header-nav-item">
|
|
|
110 <a class="header-nav-link" href="/features" data-ga-click="(Logged out) Header, go to features, text:features">Features</a>
|
|
|
111 </li>
|
|
|
112 <li class="header-nav-item">
|
|
|
113 <a class="header-nav-link" href="https://enterprise.github.com/" data-ga-click="(Logged out) Header, go to enterprise, text:enterprise">Enterprise</a>
|
|
|
114 </li>
|
|
|
115 <li class="header-nav-item">
|
|
|
116 <a class="header-nav-link" href="/blog" data-ga-click="(Logged out) Header, go to blog, text:blog">Blog</a>
|
|
|
117 </li>
|
|
|
118 </ul>
|
|
|
119
|
|
|
120 </div>
|
|
|
121 </div>
|
|
|
122
|
|
|
123
|
|
|
124
|
|
|
125 <div id="start-of-content" class="accessibility-aid"></div>
|
|
|
126 <div class="site" itemscope itemtype="http://schema.org/WebPage">
|
|
|
127 <div id="js-flash-container">
|
|
|
128
|
|
|
129 </div>
|
|
|
130 <div class="pagehead repohead instapaper_ignore readability-menu">
|
|
|
131 <div class="container">
|
|
|
132
|
|
|
133 <ul class="pagehead-actions">
|
|
|
134
|
|
|
135 <li>
|
|
|
136 <a href="/login?return_to=%2Fvipints%2FGFFtools-GX"
|
|
|
137 class="btn btn-sm btn-with-count tooltipped tooltipped-n"
|
|
|
138 aria-label="You must be signed in to watch a repository" rel="nofollow">
|
|
|
139 <span class="octicon octicon-eye"></span>
|
|
|
140 Watch
|
|
|
141 </a>
|
|
|
142 <a class="social-count" href="/vipints/GFFtools-GX/watchers">
|
|
|
143 2
|
|
|
144 </a>
|
|
|
145
|
|
|
146 </li>
|
|
|
147
|
|
|
148 <li>
|
|
|
149 <a href="/login?return_to=%2Fvipints%2FGFFtools-GX"
|
|
|
150 class="btn btn-sm btn-with-count tooltipped tooltipped-n"
|
|
|
151 aria-label="You must be signed in to star a repository" rel="nofollow">
|
|
|
152 <span class="octicon octicon-star"></span>
|
|
|
153 Star
|
|
|
154 </a>
|
|
|
155
|
|
|
156 <a class="social-count js-social-count" href="/vipints/GFFtools-GX/stargazers">
|
|
|
157 1
|
|
|
158 </a>
|
|
|
159
|
|
|
160 </li>
|
|
|
161
|
|
|
162 <li>
|
|
|
163 <a href="/login?return_to=%2Fvipints%2FGFFtools-GX"
|
|
|
164 class="btn btn-sm btn-with-count tooltipped tooltipped-n"
|
|
|
165 aria-label="You must be signed in to fork a repository" rel="nofollow">
|
|
|
166 <span class="octicon octicon-repo-forked"></span>
|
|
|
167 Fork
|
|
|
168 </a>
|
|
|
169 <a href="/vipints/GFFtools-GX/network" class="social-count">
|
|
|
170 0
|
|
|
171 </a>
|
|
|
172 </li>
|
|
|
173 </ul>
|
|
|
174
|
|
|
175 <h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public">
|
|
|
176 <span class="mega-octicon octicon-repo"></span>
|
|
|
177 <span class="author"><a href="/vipints" class="url fn" itemprop="url" rel="author"><span itemprop="title">vipints</span></a></span><!--
|
|
|
178 --><span class="path-divider">/</span><!--
|
|
|
179 --><strong><a href="/vipints/GFFtools-GX" class="js-current-repository" data-pjax="#js-repo-pjax-container">GFFtools-GX</a></strong>
|
|
|
180
|
|
|
181 <span class="page-context-loader">
|
|
|
182 <img alt="" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
183 </span>
|
|
|
184
|
|
|
185 </h1>
|
|
|
186 </div><!-- /.container -->
|
|
|
187 </div><!-- /.repohead -->
|
|
|
188
|
|
|
189 <div class="container">
|
|
|
190 <div class="repository-with-sidebar repo-container new-discussion-timeline with-full-navigation ">
|
|
|
191 <div class="repository-sidebar clearfix">
|
|
|
192
|
|
|
193 <nav class="sunken-menu repo-nav js-repo-nav js-sidenav-container-pjax js-octicon-loaders"
|
|
|
194 role="navigation"
|
|
|
195 data-pjax="#js-repo-pjax-container"
|
|
|
196 data-issue-count-url="/vipints/GFFtools-GX/issues/counts">
|
|
|
197 <ul class="sunken-menu-group">
|
|
|
198 <li class="tooltipped tooltipped-w" aria-label="Code">
|
|
|
199 <a href="/vipints/GFFtools-GX" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /vipints/GFFtools-GX">
|
|
|
200 <span class="octicon octicon-code"></span> <span class="full-word">Code</span>
|
|
|
201 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
202 </a> </li>
|
|
|
203
|
|
|
204 <li class="tooltipped tooltipped-w" aria-label="Issues">
|
|
|
205 <a href="/vipints/GFFtools-GX/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /vipints/GFFtools-GX/issues">
|
|
|
206 <span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span>
|
|
|
207 <span class="js-issue-replace-counter"></span>
|
|
|
208 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
209 </a> </li>
|
|
|
210
|
|
|
211 <li class="tooltipped tooltipped-w" aria-label="Pull requests">
|
|
|
212 <a href="/vipints/GFFtools-GX/pulls" aria-label="Pull requests" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g p" data-selected-links="repo_pulls /vipints/GFFtools-GX/pulls">
|
|
|
213 <span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull requests</span>
|
|
|
214 <span class="js-pull-replace-counter"></span>
|
|
|
215 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
216 </a> </li>
|
|
|
217
|
|
|
218 </ul>
|
|
|
219 <div class="sunken-menu-separator"></div>
|
|
|
220 <ul class="sunken-menu-group">
|
|
|
221
|
|
|
222 <li class="tooltipped tooltipped-w" aria-label="Pulse">
|
|
|
223 <a href="/vipints/GFFtools-GX/pulse" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-selected-links="pulse /vipints/GFFtools-GX/pulse">
|
|
|
224 <span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span>
|
|
|
225 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
226 </a> </li>
|
|
|
227
|
|
|
228 <li class="tooltipped tooltipped-w" aria-label="Graphs">
|
|
|
229 <a href="/vipints/GFFtools-GX/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-selected-links="repo_graphs repo_contributors /vipints/GFFtools-GX/graphs">
|
|
|
230 <span class="octicon octicon-graph"></span> <span class="full-word">Graphs</span>
|
|
|
231 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
232 </a> </li>
|
|
|
233 </ul>
|
|
|
234
|
|
|
235
|
|
|
236 </nav>
|
|
|
237
|
|
|
238 <div class="only-with-full-nav">
|
|
|
239
|
|
|
240 <div class="clone-url open"
|
|
|
241 data-protocol-type="http"
|
|
|
242 data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone">
|
|
|
243 <h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
|
|
|
244 <div class="input-group js-zeroclipboard-container">
|
|
|
245 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
|
246 value="https://github.com/vipints/GFFtools-GX.git" readonly="readonly">
|
|
|
247 <span class="input-group-button">
|
|
|
248 <button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
|
249 </span>
|
|
|
250 </div>
|
|
|
251 </div>
|
|
|
252
|
|
|
253
|
|
|
254 <div class="clone-url "
|
|
|
255 data-protocol-type="subversion"
|
|
|
256 data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone">
|
|
|
257 <h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
|
|
|
258 <div class="input-group js-zeroclipboard-container">
|
|
|
259 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
|
260 value="https://github.com/vipints/GFFtools-GX" readonly="readonly">
|
|
|
261 <span class="input-group-button">
|
|
|
262 <button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
|
263 </span>
|
|
|
264 </div>
|
|
|
265 </div>
|
|
|
266
|
|
|
267
|
|
|
268
|
|
|
269 <p class="clone-options">You can clone with
|
|
|
270 <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a> or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>.
|
|
|
271 <a href="https://help.github.com/articles/which-remote-url-should-i-use" class="help tooltipped tooltipped-n" aria-label="Get help on which URL is right for you.">
|
|
|
272 <span class="octicon octicon-question"></span>
|
|
|
273 </a>
|
|
|
274 </p>
|
|
|
275
|
|
|
276
|
|
|
277
|
|
|
278
|
|
|
279 <a href="/vipints/GFFtools-GX/archive/master.zip"
|
|
|
280 class="btn btn-sm sidebar-button"
|
|
|
281 aria-label="Download the contents of vipints/GFFtools-GX as a zip file"
|
|
|
282 title="Download the contents of vipints/GFFtools-GX as a zip file"
|
|
|
283 rel="nofollow">
|
|
|
284 <span class="octicon octicon-cloud-download"></span>
|
|
|
285 Download ZIP
|
|
|
286 </a>
|
|
|
287 </div>
|
|
|
288 </div><!-- /.repository-sidebar -->
|
|
|
289
|
|
|
290 <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container>
|
|
|
291
|
|
|
292 <span id="js-show-full-navigation"></span>
|
|
|
293
|
|
|
294 <div class="repository-meta js-details-container ">
|
|
|
295 <div class="repository-description">
|
|
|
296 gfftools - Galaxy toolshed repository
|
|
|
297 </div>
|
|
|
298
|
|
|
299
|
|
|
300
|
|
|
301 </div>
|
|
|
302
|
|
|
303 <div class="overall-summary overall-summary-bottomless">
|
|
|
304
|
|
|
305 <div class="stats-switcher-viewport js-stats-switcher-viewport">
|
|
|
306 <div class="stats-switcher-wrapper">
|
|
|
307 <ul class="numbers-summary">
|
|
|
308 <li class="commits">
|
|
|
309 <a data-pjax href="/vipints/GFFtools-GX/commits/master">
|
|
|
310 <span class="octicon octicon-history"></span>
|
|
|
311 <span class="num text-emphasized">
|
|
|
312 103
|
|
|
313 </span>
|
|
|
314 commits
|
|
|
315 </a>
|
|
|
316 </li>
|
|
|
317 <li>
|
|
|
318 <a data-pjax href="/vipints/GFFtools-GX/branches">
|
|
|
319 <span class="octicon octicon-git-branch"></span>
|
|
|
320 <span class="num text-emphasized">
|
|
|
321 1
|
|
|
322 </span>
|
|
|
323 branch
|
|
|
324 </a>
|
|
|
325 </li>
|
|
|
326
|
|
|
327 <li>
|
|
|
328 <a data-pjax href="/vipints/GFFtools-GX/releases">
|
|
|
329 <span class="octicon octicon-tag"></span>
|
|
|
330 <span class="num text-emphasized">
|
|
|
331 0
|
|
|
332 </span>
|
|
|
333 releases
|
|
|
334 </a>
|
|
|
335 </li>
|
|
|
336
|
|
|
337 <li>
|
|
|
338
|
|
|
339 <a href="/vipints/GFFtools-GX/graphs/contributors">
|
|
|
340 <span class="octicon octicon-organization"></span>
|
|
|
341 <span class="num text-emphasized">
|
|
|
342 1
|
|
|
343 </span>
|
|
|
344 contributor
|
|
|
345 </a>
|
|
|
346 </li>
|
|
|
347 </ul>
|
|
|
348
|
|
|
349 <div class="repository-lang-stats">
|
|
|
350 <ol class="repository-lang-stats-numbers">
|
|
|
351 <li>
|
|
|
352 <a href="/vipints/GFFtools-GX/search?l=python">
|
|
|
353 <span class="color-block language-color" style="background-color:#3581ba;"></span>
|
|
|
354 <span class="lang">Python</span>
|
|
|
355 <span class="percent">100%</span>
|
|
|
356 </a>
|
|
|
357 </li>
|
|
|
358 </ol>
|
|
|
359 </div>
|
|
|
360 </div>
|
|
|
361 </div>
|
|
|
362
|
|
|
363 </div>
|
|
|
364
|
|
|
365 <div class="repository-lang-stats-graph js-toggle-lang-stats" title="Click for language details">
|
|
|
366 <span class="language-color" aria-label="Python 100%" style="width:100%; background-color:#3581ba;" itemprop="keywords">Python</span>
|
|
|
367 </div>
|
|
|
368
|
|
|
369 <include-fragment src="/vipints/GFFtools-GX/show_partial?partial=recently_touched_branches_list"></include-fragment>
|
|
|
370
|
|
|
371 <div class="file-navigation in-mid-page">
|
|
|
372 <a href="/vipints/GFFtools-GX/find/master"
|
|
|
373 class="js-show-file-finder btn btn-sm empty-icon tooltipped tooltipped-s right"
|
|
|
374 data-pjax
|
|
|
375 data-hotkey="t"
|
|
|
376 aria-label="Quickly jump between files">
|
|
|
377 <span class="octicon octicon-list-unordered"></span>
|
|
|
378 </a>
|
|
|
379 <a href="/vipints/GFFtools-GX/compare" aria-label="Compare, review, create a pull request" class="btn btn-sm btn-primary tooltipped tooltipped-se left compare-button" aria-label="Compare & review" data-pjax data-ga-click="Repository, go to compare view, location:repo overview; icon:git-compare">
|
|
|
380 <span class="octicon octicon-git-compare"></span>
|
|
|
381 </a>
|
|
|
382
|
|
|
383
|
|
|
384 <div class="select-menu js-menu-container js-select-menu left">
|
|
|
385 <span class="btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w"
|
|
|
386 data-master-branch="master"
|
|
|
387 data-ref="master"
|
|
|
388 title="master"
|
|
|
389 role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true">
|
|
|
390 <span class="octicon octicon-git-branch"></span>
|
|
|
391 <i>branch:</i>
|
|
|
392 <span class="js-select-button css-truncate-target">master</span>
|
|
|
393 </span>
|
|
|
394
|
|
|
395 <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true">
|
|
|
396
|
|
|
397 <div class="select-menu-modal">
|
|
|
398 <div class="select-menu-header">
|
|
|
399 <span class="select-menu-title">Switch branches/tags</span>
|
|
|
400 <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
|
|
|
401 </div>
|
|
|
402
|
|
|
403 <div class="select-menu-filters">
|
|
|
404 <div class="select-menu-text-filter">
|
|
|
405 <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags">
|
|
|
406 </div>
|
|
|
407 <div class="select-menu-tabs">
|
|
|
408 <ul>
|
|
|
409 <li class="select-menu-tab">
|
|
|
410 <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab">Branches</a>
|
|
|
411 </li>
|
|
|
412 <li class="select-menu-tab">
|
|
|
413 <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tagโฆ" class="js-select-menu-tab">Tags</a>
|
|
|
414 </li>
|
|
|
415 </ul>
|
|
|
416 </div>
|
|
|
417 </div>
|
|
|
418
|
|
|
419 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches">
|
|
|
420
|
|
|
421 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
|
|
|
422
|
|
|
423
|
|
|
424 <a class="select-menu-item js-navigation-item js-navigation-open selected"
|
|
|
425 href="/vipints/GFFtools-GX/tree/master"
|
|
|
426 data-name="master"
|
|
|
427 data-skip-pjax="true"
|
|
|
428 rel="nofollow">
|
|
|
429 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
|
430 <span class="select-menu-item-text css-truncate-target" title="master">
|
|
|
431 master
|
|
|
432 </span>
|
|
|
433 </a>
|
|
|
434 </div>
|
|
|
435
|
|
|
436 <div class="select-menu-no-results">Nothing to show</div>
|
|
|
437 </div>
|
|
|
438
|
|
|
439 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags">
|
|
|
440 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
|
|
|
441
|
|
|
442
|
|
|
443 </div>
|
|
|
444
|
|
|
445 <div class="select-menu-no-results">Nothing to show</div>
|
|
|
446 </div>
|
|
|
447
|
|
|
448 </div>
|
|
|
449 </div>
|
|
|
450 </div>
|
|
|
451
|
|
|
452
|
|
|
453
|
|
|
454 <div class="breadcrumb"><span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/vipints/GFFtools-GX" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">GFFtools-GX</span></a></span></span><span class="separator">/</span>
|
|
|
455 <a class="btn-link disabled tooltipped tooltipped-e" href="#" aria-label="You must be signed in to make or propose changes">
|
|
|
456 <span class="octicon octicon-plus"></span>
|
|
|
457 </a>
|
|
|
458 </div>
|
|
|
459 </div>
|
|
|
460
|
|
|
461
|
|
|
462
|
|
|
463
|
|
|
464 <div class="commit commit-tease js-details-container" >
|
|
|
465 <p class="commit-title ">
|
|
|
466 <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="message" data-pjax="true" title="fixed">fixed</a>
|
|
|
467
|
|
|
468 </p>
|
|
|
469 <div class="commit-meta">
|
|
|
470 <button aria-label="Copy SHA" class="js-zeroclipboard zeroclipboard-link tooltipped tooltipped-s" data-clipboard-text="0ea921f8d7cc65bb044616b14dfdae59b54e2073" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
|
471 <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="sha-block" data-pjax>latest commit <span class="sha">0ea921f8d7</span></a>
|
|
|
472
|
|
|
473 <div class="authorship">
|
|
|
474 <img alt="@vipints" class="avatar" data-user="1714549" height="20" src="https://avatars0.githubusercontent.com/u/1714549?v=3&s=40" width="20" />
|
|
|
475 <span class="author-name"><a href="/vipints" rel="author">vipints</a></span>
|
|
|
476 authored <time class="updated" datetime="2015-04-23T21:27:17Z" is="relative-time">Apr 23, 2015</time>
|
|
|
477
|
|
|
478 </div>
|
|
|
479 </div>
|
|
|
480 </div>
|
|
|
481
|
|
|
482
|
|
|
483 <div class="file-wrap">
|
|
|
484 <a href="/vipints/GFFtools-GX/tree/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a>
|
|
|
485
|
|
|
486 <table class="files" data-pjax>
|
|
|
487
|
|
|
488
|
|
|
489 <tbody>
|
|
|
490 <tr class="warning include-fragment-error">
|
|
|
491 <td class="icon"><span class="octicon octicon-alert"></span></td>
|
|
|
492 <td class="content" colspan="3">Failed to load latest commit information.</td>
|
|
|
493 </tr>
|
|
|
494
|
|
|
495 <tr>
|
|
|
496 <td class="icon">
|
|
|
497 <span class="octicon octicon-file-directory"></span>
|
|
|
498 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
499 </td>
|
|
|
500 <td class="content">
|
|
|
501 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/tree/master/test-data" class="js-directory-link" id="24346e1b50066607059af36e3b684b24-99e7a2029aade02cb90a0e26ff6109547a6078ea" title="test-data">test-data</a></span>
|
|
|
502 </td>
|
|
|
503 <td class="message">
|
|
|
504 <span class="css-truncate css-truncate-target">
|
|
|
505 <a href="/vipints/GFFtools-GX/commit/46e670f9d93f3797740d21a100428fe195b6c83f" class="message" data-pjax="true" title="functional test perfomed after the change">functional test perfomed after the change</a>
|
|
|
506 </span>
|
|
|
507 </td>
|
|
|
508 <td class="age">
|
|
|
509 <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:42:01Z" is="time-ago">Apr 21, 2015</time></span>
|
|
|
510 </td>
|
|
|
511 </tr>
|
|
|
512 <tr>
|
|
|
513 <td class="icon">
|
|
|
514 <span class="octicon octicon-file-text"></span>
|
|
|
515 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
516 </td>
|
|
|
517 <td class="content">
|
|
|
518 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/.gitignore" class="js-directory-link" id="a084b794bc0759e7a6b77810e01874f2-0334fc9da4d9b7a262012ae6cae37002259af5b2" title=".gitignore">.gitignore</a></span>
|
|
|
519 </td>
|
|
|
520 <td class="message">
|
|
|
521 <span class="css-truncate css-truncate-target">
|
|
|
522 <a href="/vipints/GFFtools-GX/commit/c5b661defaf94700cf290651669846c8258e220d" class="message" data-pjax="true" title="ignored pyc and swap files">ignored pyc and swap files</a>
|
|
|
523 </span>
|
|
|
524 </td>
|
|
|
525 <td class="age">
|
|
|
526 <span class="css-truncate css-truncate-target"><time datetime="2014-07-18T22:28:50Z" is="time-ago">Jul 18, 2014</time></span>
|
|
|
527 </td>
|
|
|
528 </tr>
|
|
|
529 <tr>
|
|
|
530 <td class="icon">
|
|
|
531 <span class="octicon octicon-file-text"></span>
|
|
|
532 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
533 </td>
|
|
|
534 <td class="content">
|
|
|
535 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/GFFParser.py" class="js-directory-link" id="4a9c2f3a2b51d00c039e9951aa5df3fd-505eece57e21af803c93cdb06d9d569c81d1d811" title="GFFParser.py">GFFParser.py</a></span>
|
|
|
536 </td>
|
|
|
537 <td class="message">
|
|
|
538 <span class="css-truncate css-truncate-target">
|
|
|
539 <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF fโฆ</a>
|
|
|
540 </span>
|
|
|
541 </td>
|
|
|
542 <td class="age">
|
|
|
543 <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span>
|
|
|
544 </td>
|
|
|
545 </tr>
|
|
|
546 <tr>
|
|
|
547 <td class="icon">
|
|
|
548 <span class="octicon octicon-file-text"></span>
|
|
|
549 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
550 </td>
|
|
|
551 <td class="content">
|
|
|
552 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/README.md" class="js-directory-link" id="04c6e90faac2675aa89e2176d2eec7d8-17e766c0f2926d94933cb7320afd6c1f5db293fb" title="README.md">README.md</a></span>
|
|
|
553 </td>
|
|
|
554 <td class="message">
|
|
|
555 <span class="css-truncate css-truncate-target">
|
|
|
556 <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="message" data-pjax="true" title="fixed">fixed</a>
|
|
|
557 </span>
|
|
|
558 </td>
|
|
|
559 <td class="age">
|
|
|
560 <span class="css-truncate css-truncate-target"><time datetime="2015-04-23T21:27:17Z" is="time-ago">Apr 23, 2015</time></span>
|
|
|
561 </td>
|
|
|
562 </tr>
|
|
|
563 <tr>
|
|
|
564 <td class="icon">
|
|
|
565 <span class="octicon octicon-file-text"></span>
|
|
|
566 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
567 </td>
|
|
|
568 <td class="content">
|
|
|
569 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.py" class="js-directory-link" id="4fd14b034003e6ed6b3c1243f3f285ed-461ae7292d229b40fb98dec1d28a67aebfde7c96" title="bed_to_gff.py">bed_to_gff.py</a></span>
|
|
|
570 </td>
|
|
|
571 <td class="message">
|
|
|
572 <span class="css-truncate css-truncate-target">
|
|
|
573 <a href="/vipints/GFFtools-GX/commit/b882fc8c206c3203792da6c4c856005eb06934c4" class="message" data-pjax="true" title="removing print statement from the code">removing print statement from the code</a>
|
|
|
574 </span>
|
|
|
575 </td>
|
|
|
576 <td class="age">
|
|
|
577 <span class="css-truncate css-truncate-target"><time datetime="2015-04-14T23:41:11Z" is="time-ago">Apr 14, 2015</time></span>
|
|
|
578 </td>
|
|
|
579 </tr>
|
|
|
580 <tr>
|
|
|
581 <td class="icon">
|
|
|
582 <span class="octicon octicon-file-text"></span>
|
|
|
583 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
584 </td>
|
|
|
585 <td class="content">
|
|
|
586 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.xml" class="js-directory-link" id="fd45df94f6d642a741c0c8d038949b37-2b5908455dd6730bd4bbd634f56316dfd70eca03" title="bed_to_gff.xml">bed_to_gff.xml</a></span>
|
|
|
587 </td>
|
|
|
588 <td class="message">
|
|
|
589 <span class="css-truncate css-truncate-target">
|
|
|
590 <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a>
|
|
|
591 </span>
|
|
|
592 </td>
|
|
|
593 <td class="age">
|
|
|
594 <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span>
|
|
|
595 </td>
|
|
|
596 </tr>
|
|
|
597 <tr>
|
|
|
598 <td class="icon">
|
|
|
599 <span class="octicon octicon-file-text"></span>
|
|
|
600 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
601 </td>
|
|
|
602 <td class="content">
|
|
|
603 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.py" class="js-directory-link" id="8cedf4409efd74682d25ee79bb3574dc-6638d994bf8d1a8aaa231c70bf44b6021f9ccf1b" title="gbk_to_gff.py">gbk_to_gff.py</a></span>
|
|
|
604 </td>
|
|
|
605 <td class="message">
|
|
|
606 <span class="css-truncate css-truncate-target">
|
|
|
607 <a href="/vipints/GFFtools-GX/commit/84a145c7ee9efa171dbe1d64223e20ceb1930de6" class="message" data-pjax="true" title="gbk parsing and correctly assigning feature type">gbk parsing and correctly assigning feature type</a>
|
|
|
608 </span>
|
|
|
609 </td>
|
|
|
610 <td class="age">
|
|
|
611 <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:04:25Z" is="time-ago">Apr 17, 2015</time></span>
|
|
|
612 </td>
|
|
|
613 </tr>
|
|
|
614 <tr>
|
|
|
615 <td class="icon">
|
|
|
616 <span class="octicon octicon-file-text"></span>
|
|
|
617 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
618 </td>
|
|
|
619 <td class="content">
|
|
|
620 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.xml" class="js-directory-link" id="5e708155a06e4244e26c978ed02c6fd2-c90e390761eb5390bda2e245b7eb7456d5e9c665" title="gbk_to_gff.xml">gbk_to_gff.xml</a></span>
|
|
|
621 </td>
|
|
|
622 <td class="message">
|
|
|
623 <span class="css-truncate css-truncate-target">
|
|
|
624 <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a>
|
|
|
625 </span>
|
|
|
626 </td>
|
|
|
627 <td class="age">
|
|
|
628 <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span>
|
|
|
629 </td>
|
|
|
630 </tr>
|
|
|
631 <tr>
|
|
|
632 <td class="icon">
|
|
|
633 <span class="octicon octicon-file-text"></span>
|
|
|
634 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
635 </td>
|
|
|
636 <td class="content">
|
|
|
637 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.py" class="js-directory-link" id="95b17a03c0948b20d1264fcd269b60fa-457e6d44dbc1f4531de174641f74f9e6ec689982" title="gff_to_bed.py">gff_to_bed.py</a></span>
|
|
|
638 </td>
|
|
|
639 <td class="message">
|
|
|
640 <span class="css-truncate css-truncate-target">
|
|
|
641 <a href="/vipints/GFFtools-GX/commit/f84e0d96db79436b685066c088bf1555a3bf29e1" class="message" data-pjax="true" title="changing the float behaviour to int">changing the float behaviour to int</a>
|
|
|
642 </span>
|
|
|
643 </td>
|
|
|
644 <td class="age">
|
|
|
645 <span class="css-truncate css-truncate-target"><time datetime="2015-04-22T16:25:13Z" is="time-ago">Apr 22, 2015</time></span>
|
|
|
646 </td>
|
|
|
647 </tr>
|
|
|
648 <tr>
|
|
|
649 <td class="icon">
|
|
|
650 <span class="octicon octicon-file-text"></span>
|
|
|
651 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
652 </td>
|
|
|
653 <td class="content">
|
|
|
654 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.xml" class="js-directory-link" id="8c7d5ae4b79728262acfc56888f2444e-10754bece6a7a5a7c5dc9d533d92ddfa046e6b6b" title="gff_to_bed.xml">gff_to_bed.xml</a></span>
|
|
|
655 </td>
|
|
|
656 <td class="message">
|
|
|
657 <span class="css-truncate css-truncate-target">
|
|
|
658 <a href="/vipints/GFFtools-GX/commit/2c96e399526d372a61df5b4068bc91e08af49092" class="message" data-pjax="true" title="updated the wrapper version">updated the wrapper version</a>
|
|
|
659 </span>
|
|
|
660 </td>
|
|
|
661 <td class="age">
|
|
|
662 <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T02:59:32Z" is="time-ago">Apr 18, 2015</time></span>
|
|
|
663 </td>
|
|
|
664 </tr>
|
|
|
665 <tr>
|
|
|
666 <td class="icon">
|
|
|
667 <span class="octicon octicon-file-text"></span>
|
|
|
668 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
669 </td>
|
|
|
670 <td class="content">
|
|
|
671 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.py" class="js-directory-link" id="88b7a441373dfec1e07cd28bb1eb8c3e-9ff53c56125edfa286255f489e61cda154a21693" title="gff_to_gtf.py">gff_to_gtf.py</a></span>
|
|
|
672 </td>
|
|
|
673 <td class="message">
|
|
|
674 <span class="css-truncate css-truncate-target">
|
|
|
675 <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a>
|
|
|
676 </span>
|
|
|
677 </td>
|
|
|
678 <td class="age">
|
|
|
679 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span>
|
|
|
680 </td>
|
|
|
681 </tr>
|
|
|
682 <tr>
|
|
|
683 <td class="icon">
|
|
|
684 <span class="octicon octicon-file-text"></span>
|
|
|
685 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
686 </td>
|
|
|
687 <td class="content">
|
|
|
688 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.xml" class="js-directory-link" id="f4676750a1f71b9fbf35b537b0546842-a2b41ec7924d6609f219bdf8c0372af59ea747d2" title="gff_to_gtf.xml">gff_to_gtf.xml</a></span>
|
|
|
689 </td>
|
|
|
690 <td class="message">
|
|
|
691 <span class="css-truncate css-truncate-target">
|
|
|
692 <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a>
|
|
|
693 </span>
|
|
|
694 </td>
|
|
|
695 <td class="age">
|
|
|
696 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span>
|
|
|
697 </td>
|
|
|
698 </tr>
|
|
|
699 <tr>
|
|
|
700 <td class="icon">
|
|
|
701 <span class="octicon octicon-file-text"></span>
|
|
|
702 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
703 </td>
|
|
|
704 <td class="content">
|
|
|
705 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.py" class="js-directory-link" id="6989ac39182645599caeb47b4e0e8ef6-6d786691f74f0c00db3da883f4e6e7e1d009d2c2" title="gtf_to_gff.py">gtf_to_gff.py</a></span>
|
|
|
706 </td>
|
|
|
707 <td class="message">
|
|
|
708 <span class="css-truncate css-truncate-target">
|
|
|
709 <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a>
|
|
|
710 </span>
|
|
|
711 </td>
|
|
|
712 <td class="age">
|
|
|
713 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span>
|
|
|
714 </td>
|
|
|
715 </tr>
|
|
|
716 <tr>
|
|
|
717 <td class="icon">
|
|
|
718 <span class="octicon octicon-file-text"></span>
|
|
|
719 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
720 </td>
|
|
|
721 <td class="content">
|
|
|
722 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.xml" class="js-directory-link" id="a8bd25db400514c2556192045eacd820-dc2031de1c3daa1cf8644a5c62c9d4afce97ad39" title="gtf_to_gff.xml">gtf_to_gff.xml</a></span>
|
|
|
723 </td>
|
|
|
724 <td class="message">
|
|
|
725 <span class="css-truncate css-truncate-target">
|
|
|
726 <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a>
|
|
|
727 </span>
|
|
|
728 </td>
|
|
|
729 <td class="age">
|
|
|
730 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span>
|
|
|
731 </td>
|
|
|
732 </tr>
|
|
|
733 <tr>
|
|
|
734 <td class="icon">
|
|
|
735 <span class="octicon octicon-file-text"></span>
|
|
|
736 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
737 </td>
|
|
|
738 <td class="content">
|
|
|
739 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/helper.py" class="js-directory-link" id="702b6abf015bfdb4e41308ddd3b297a9-a711ed60defe1bd9ef579fada75e32da2313935c" title="helper.py">helper.py</a></span>
|
|
|
740 </td>
|
|
|
741 <td class="message">
|
|
|
742 <span class="css-truncate css-truncate-target">
|
|
|
743 <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF fโฆ</a>
|
|
|
744 </span>
|
|
|
745 </td>
|
|
|
746 <td class="age">
|
|
|
747 <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span>
|
|
|
748 </td>
|
|
|
749 </tr>
|
|
|
750 <tr>
|
|
|
751 <td class="icon">
|
|
|
752 <span class="octicon octicon-file-text"></span>
|
|
|
753 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
754 </td>
|
|
|
755 <td class="content">
|
|
|
756 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_conf.xml.sample" class="js-directory-link" id="76a06ab03a6f35bfb6ff2be40e654b7e-e26478f762dbc5e03f339bc5598086009e4f8be0" title="tool_conf.xml.sample">tool_conf.xml.sample</a></span>
|
|
|
757 </td>
|
|
|
758 <td class="message">
|
|
|
759 <span class="css-truncate css-truncate-target">
|
|
|
760 <a href="/vipints/GFFtools-GX/commit/04ccdc96c4bf8d6b8420a05c9afa8c8540345e32" class="message" data-pjax="true" title="updated the toolpanel list">updated the toolpanel list</a>
|
|
|
761 </span>
|
|
|
762 </td>
|
|
|
763 <td class="age">
|
|
|
764 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:15:28Z" is="time-ago">Apr 20, 2015</time></span>
|
|
|
765 </td>
|
|
|
766 </tr>
|
|
|
767 <tr>
|
|
|
768 <td class="icon">
|
|
|
769 <span class="octicon octicon-file-text"></span>
|
|
|
770 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
|
|
|
771 </td>
|
|
|
772 <td class="content">
|
|
|
773 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_dependencies.xml" class="js-directory-link" id="1f1e2fcbf1ddc07a88bc59ca246c9a90-a0a1a7f1bb7e1a6a8b79f30629c8968f8b4c8d36" title="tool_dependencies.xml">tool_dependencies.xml</a></span>
|
|
|
774 </td>
|
|
|
775 <td class="message">
|
|
|
776 <span class="css-truncate css-truncate-target">
|
|
|
777 <a href="/vipints/GFFtools-GX/commit/c75c2be2f54ca59449e999346de2427584789ec9" class="message" data-pjax="true" title="biopython required">biopython required</a>
|
|
|
778 </span>
|
|
|
779 </td>
|
|
|
780 <td class="age">
|
|
|
781 <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:54:33Z" is="time-ago">Apr 21, 2015</time></span>
|
|
|
782 </td>
|
|
|
783 </tr>
|
|
|
784 </tbody>
|
|
|
785 </table>
|
|
|
786
|
|
|
787 </div>
|
|
|
788
|
|
|
789
|
|
|
790 <div id="readme" class="boxed-group flush clearfix announce instapaper_body md">
|
|
|
791 <h3>
|
|
|
792 <span class="octicon octicon-book"></span>
|
|
|
793 README.md
|
|
|
794 </h3>
|
|
|
795
|
|
|
796 <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1>
|
|
|
797 <a id="user-content-gfftools-gx-" class="anchor" href="#gfftools-gx-" aria-hidden="true"><span class="octicon octicon-link"></span></a>GFFtools-GX </h1>
|
|
|
798
|
|
|
799 <p>A collection of tools for converting genome annotation between <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format4">GTF</a>, <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a>, <a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html">GenBank</a> and <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format3">GFF</a>.</p>
|
|
|
800
|
|
|
801 <h5>
|
|
|
802 <a id="user-content-introduction" class="anchor" href="#introduction" aria-hidden="true"><span class="octicon octicon-link"></span></a>INTRODUCTION</h5>
|
|
|
803
|
|
|
804 <p>Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like <a href="http://www.ensembl.org">ENSEMBL</a>, <a href="https://genome.ucsc.edu/">UCSC</a>, <a href="http://genome.jgi.doe.gov/">JGI</a> and <a href="http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/HelpJan.html">NCBI AceView</a>. These programs can be easily integrated into your galaxy instance.</p>
|
|
|
805
|
|
|
806 <h5>
|
|
|
807 <a id="user-content-contents" class="anchor" href="#contents" aria-hidden="true"><span class="octicon octicon-link"></span></a>CONTENTS</h5>
|
|
|
808
|
|
|
809 <p>Included utilities are: </p>
|
|
|
810
|
|
|
811 <pre><code>BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
|
|
|
812 GBK-to-GFF: convert data from genbank format to GFF
|
|
|
813 GFF-to-BED: convert data from GFF to 12 column BED format
|
|
|
814 GFF-to-GTF: convert data from GFF to GTF
|
|
|
815 GTF-to-GFF: convert data from GTF to valid GFF
|
|
|
816 </code></pre>
|
|
|
817
|
|
|
818 <p>test-data: Test data set. (move to your galaxy-root-folder/test-data/)</p>
|
|
|
819
|
|
|
820 <pre><code>You may need to move the test files into your test-data directory so galaxy can find them.
|
|
|
821 If you want to run the functional tests eg as:
|
|
|
822
|
|
|
823 exmaple:
|
|
|
824 sh run_functional_tests.sh -id fml_gtf2gff
|
|
|
825 </code></pre>
|
|
|
826
|
|
|
827 <h5>
|
|
|
828 <a id="user-content-requirements" class="anchor" href="#requirements" aria-hidden="true"><span class="octicon octicon-link"></span></a>REQUIREMENTS</h5>
|
|
|
829
|
|
|
830 <pre><code>python2.6 or 2.7 and biopython
|
|
|
831
|
|
|
832 Galaxy should be able to automatically install biopython via Galaxy toolshed.
|
|
|
833 </code></pre>
|
|
|
834
|
|
|
835 <h5>
|
|
|
836 <a id="user-content-commentsquestions" class="anchor" href="#commentsquestions" aria-hidden="true"><span class="octicon octicon-link"></span></a>COMMENTS/QUESTIONS</h5>
|
|
|
837
|
|
|
838 <p>I can be reached at vipin [at] cbio.mskcc.org </p>
|
|
|
839
|
|
|
840 <h5>
|
|
|
841 <a id="user-content-license" class="anchor" href="#license" aria-hidden="true"><span class="octicon octicon-link"></span></a>LICENSE</h5>
|
|
|
842
|
|
|
843 <p>Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society</p>
|
|
|
844
|
|
|
845 <pre><code> 2013-2015, Memorial Sloan Kettering Cancer Center
|
|
|
846 Vipin T Sreedharan <vipin@cbio.mskcc.org>
|
|
|
847 </code></pre>
|
|
|
848
|
|
|
849 <p>All rights reserved.</p>
|
|
|
850
|
|
|
851 <p>Licensed under the BSD 2-Clause License: <a href="http://opensource.org/licenses/BSD-2-Clause">http://opensource.org/licenses/BSD-2-Clause</a></p>
|
|
|
852
|
|
|
853 <pre><code>Redistribution and use in source and binary forms, with or without
|
|
|
854 modification, are permitted provided that the following conditions are met:
|
|
|
855
|
|
|
856 * Redistributions of source code must retain the above copyright notice,
|
|
|
857 this list of conditions and the following disclaimer.
|
|
|
858
|
|
|
859 * Redistributions in binary form must reproduce the above copyright notice,
|
|
|
860 this list of conditions and the following disclaimer in the documentation
|
|
|
861 and/or other materials provided with the distribution.
|
|
|
862
|
|
|
863 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
|
|
|
864 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
|
|
|
865 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
|
|
|
866 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
|
|
|
867 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
|
|
868 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
|
|
|
869 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
|
|
|
870 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
|
|
|
871 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
|
|
|
872 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
|
|
873 </code></pre>
|
|
|
874
|
|
|
875 <h5>
|
|
|
876 <a id="user-content-courtesy" class="anchor" href="#courtesy" aria-hidden="true"><span class="octicon octicon-link"></span></a>COURTESY</h5>
|
|
|
877
|
|
|
878 <p>To the Galaxy Team.</p>
|
|
|
879 </article>
|
|
|
880 </div>
|
|
|
881
|
|
|
882
|
|
|
883 </div>
|
|
|
884
|
|
|
885 </div><!-- /.repo-container -->
|
|
|
886 <div class="modal-backdrop"></div>
|
|
|
887 </div><!-- /.container -->
|
|
|
888 </div><!-- /.site -->
|
|
|
889
|
|
|
890
|
|
|
891 </div><!-- /.wrapper -->
|
|
|
892
|
|
|
893 <div class="container">
|
|
|
894 <div class="site-footer" role="contentinfo">
|
|
|
895 <ul class="site-footer-links right">
|
|
|
896 <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
|
|
|
897 <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
|
|
|
898 <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
|
|
|
899 <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li>
|
|
|
900 <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
|
|
|
901 <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li>
|
|
|
902
|
|
|
903 </ul>
|
|
|
904
|
|
|
905 <a href="https://github.com" aria-label="Homepage">
|
|
|
906 <span class="mega-octicon octicon-mark-github" title="GitHub"></span>
|
|
|
907 </a>
|
|
|
908 <ul class="site-footer-links">
|
|
|
909 <li>© 2015 <span title="0.04621s from github-fe120-cp1-prd.iad.github.net">GitHub</span>, Inc.</li>
|
|
|
910 <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li>
|
|
|
911 <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li>
|
|
|
912 <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li>
|
|
|
913 <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li>
|
|
|
914 </ul>
|
|
|
915 </div>
|
|
|
916 </div>
|
|
|
917
|
|
|
918
|
|
|
919 <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay">
|
|
|
920 <div class="fullscreen-container js-suggester-container">
|
|
|
921 <div class="textarea-wrap">
|
|
|
922 <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea>
|
|
|
923 <div class="suggester-container">
|
|
|
924 <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div>
|
|
|
925 </div>
|
|
|
926 </div>
|
|
|
927 </div>
|
|
|
928 <div class="fullscreen-sidebar">
|
|
|
929 <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode">
|
|
|
930 <span class="mega-octicon octicon-screen-normal"></span>
|
|
|
931 </a>
|
|
|
932 <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w"
|
|
|
933 aria-label="Switch themes">
|
|
|
934 <span class="octicon octicon-color-mode"></span>
|
|
|
935 </a>
|
|
|
936 </div>
|
|
|
937 </div>
|
|
|
938
|
|
|
939
|
|
|
940
|
|
|
941
|
|
|
942
|
|
|
943
|
|
|
944 <div id="ajax-error-message" class="flash flash-error">
|
|
|
945 <span class="octicon octicon-alert"></span>
|
|
|
946 <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a>
|
|
|
947 Something went wrong with that request. Please try again.
|
|
|
948 </div>
|
|
|
949
|
|
|
950
|
|
|
951 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-2c8ae50712a47d2b83d740cb875d55cdbbb3fdbccf303951cc6b7e63731e0c38.js"></script>
|
|
|
952 <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-747277110ee545263834c3918a562a2dc155e610ea48c5808df3838c3325cd60.js"></script>
|
|
|
953
|
|
|
954
|
|
|
955
|
|
|
956
|
|
|
957 </body>
|
|
|
958 </html>
|
|
|
959
|
