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 <meta name="viewport" content="width=1020">
|
|
11
|
|
12
|
|
13 <title>tools-devteam/tools/bowtie2/test-data at master ยท galaxyproject/tools-devteam</title>
|
|
14 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
|
|
15 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
|
|
16 <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png">
|
|
17 <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png">
|
|
18 <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png">
|
|
19 <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144.png">
|
|
20 <meta property="fb:app_id" content="1401488693436528">
|
|
21
|
|
22 <meta content="@github" name="twitter:site" /><meta content="summary" name="twitter:card" /><meta content="galaxyproject/tools-devteam" name="twitter:title" /><meta content="tools-devteam - Contains a set of Galaxy Tools mostly written by the Galaxy Team." name="twitter:description" /><meta content="https://avatars2.githubusercontent.com/u/7937847?v=3&s=400" name="twitter:image:src" />
|
|
23 <meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars2.githubusercontent.com/u/7937847?v=3&s=400" property="og:image" /><meta content="galaxyproject/tools-devteam" property="og:title" /><meta content="https://github.com/galaxyproject/tools-devteam" property="og:url" /><meta content="tools-devteam - Contains a set of Galaxy Tools mostly written by the Galaxy Team." property="og:description" />
|
|
24 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
|
|
25 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
|
|
26 <link rel="assets" href="https://assets-cdn.github.com/">
|
|
27 <link rel="web-socket" href="wss://live.github.com/_sockets/OTc3Njk3Nzo0M2VmMGIwODU0ZjU3ZWUxZThhZWIwMzY1MjMxOTE1ODo4ZTQ0Y2E0ODgwZDM3MTJiNWRhNWVlOTUyOGM5ODNlNTZhZjQxMDQ5MDYwYzU0ZGY5NTY5Mzc1YTJkOTNkNjYw--f73b909c7c1527a9b16c59ffb4ec09a14213234b">
|
|
28 <meta name="pjax-timeout" content="1000">
|
|
29 <link rel="sudo-modal" href="/sessions/sudo_modal">
|
|
30
|
|
31 <meta name="msapplication-TileImage" content="/windows-tile.png">
|
|
32 <meta name="msapplication-TileColor" content="#ffffff">
|
|
33 <meta name="selected-link" value="repo_source" data-pjax-transient>
|
|
34
|
|
35 <meta name="google-analytics" content="UA-3769691-2">
|
|
36
|
|
37 <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="8B854312:44D5:94885B4:55BF2BA5" name="octolytics-dimension-request_id" /><meta content="9776977" name="octolytics-actor-id" /><meta content="Eduardo-Alves" name="octolytics-actor-login" /><meta content="b1558c41543f659c70990998ad85b957c250a8165ce75605b88cc78511c02670" name="octolytics-actor-hash" />
|
|
38
|
|
39 <meta content="Rails, view, files#disambiguate" data-pjax-transient="true" name="analytics-event" />
|
|
40 <meta class="js-ga-set" name="dimension1" content="Logged In">
|
|
41 <meta class="js-ga-set" name="dimension4" content="Current repo nav">
|
|
42 <meta name="is-dotcom" content="true">
|
|
43 <meta name="hostname" content="github.com">
|
|
44 <meta name="user-login" content="Eduardo-Alves">
|
|
45
|
|
46 <link rel="icon" sizes="any" mask href="https://assets-cdn.github.com/pinned-octocat.svg">
|
|
47 <meta name="theme-color" content="#4078c0">
|
|
48 <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico">
|
|
49
|
|
50 <!-- </textarea> --><!-- '"` --><meta content="authenticity_token" name="csrf-param" />
|
|
51 <meta content="sIPcOPJvZdTd08u39MkUQ/PUyKwsCvX894Dnj44snbI93uW0BUf/KxzFCKGGP95A7rkJXNTeIYkid/7aVVwPVA==" name="csrf-token" />
|
|
52
|
|
53
|
|
54 <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github/index-c7126cd67871e693a9f863b7a0e99879ca39079b15a8784f8b543c03bf14ad72.css" media="all" rel="stylesheet" />
|
|
55 <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github2/index-87247f16e6450ef54cb0eda3f8f1484e33a3f18c7a7d3df1f76f67cba36a8d6d.css" media="all" rel="stylesheet" />
|
|
56
|
|
57
|
|
58
|
|
59
|
|
60 <meta http-equiv="x-pjax-version" content="f8fdf7d6713452aadb5c847c2e94f51b">
|
|
61
|
|
62
|
|
63 <meta name="description" content="tools-devteam - Contains a set of Galaxy Tools mostly written by the Galaxy Team.">
|
|
64 <meta name="go-import" content="github.com/galaxyproject/tools-devteam git https://github.com/galaxyproject/tools-devteam.git">
|
|
65
|
|
66 <meta content="7937847" name="octolytics-dimension-user_id" /><meta content="galaxyproject" name="octolytics-dimension-user_login" /><meta content="24609401" name="octolytics-dimension-repository_id" /><meta content="galaxyproject/tools-devteam" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="24609401" name="octolytics-dimension-repository_network_root_id" /><meta content="galaxyproject/tools-devteam" name="octolytics-dimension-repository_network_root_nwo" />
|
|
67 <link href="https://github.com/galaxyproject/tools-devteam/commits/master.atom" rel="alternate" title="Recent Commits to tools-devteam:master" type="application/atom+xml">
|
|
68
|
|
69 </head>
|
|
70
|
|
71
|
|
72 <body class="logged_in env-production linux vis-public">
|
|
73 <a href="#start-of-content" tabindex="1" class="accessibility-aid js-skip-to-content">Skip to content</a>
|
|
74 <div class="wrapper">
|
|
75
|
|
76
|
|
77
|
|
78
|
|
79
|
|
80
|
|
81 <div class="header header-logged-in true" role="banner">
|
|
82 <div class="container clearfix">
|
|
83
|
|
84 <a class="header-logo-invertocat" href="https://github.com/" data-hotkey="g d" aria-label="Homepage" data-ga-click="Header, go to dashboard, icon:logo">
|
|
85 <span class="mega-octicon octicon-mark-github"></span>
|
|
86 </a>
|
|
87
|
|
88
|
|
89 <div class="site-search repo-scope js-site-search" role="search">
|
|
90 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/galaxyproject/tools-devteam/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/galaxyproject/tools-devteam/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div>
|
|
91 <label class="js-chromeless-input-container form-control">
|
|
92 <div class="scope-badge">This repository</div>
|
|
93 <input type="text"
|
|
94 class="js-site-search-focus js-site-search-field is-clearable chromeless-input"
|
|
95 data-hotkey="s"
|
|
96 name="q"
|
|
97 placeholder="Search"
|
|
98 aria-label="Search this repository"
|
|
99 data-global-scope-placeholder="Search GitHub"
|
|
100 data-repo-scope-placeholder="Search"
|
|
101 tabindex="1"
|
|
102 autocapitalize="off">
|
|
103 </label>
|
|
104 </form>
|
|
105 </div>
|
|
106
|
|
107 <ul class="header-nav left" role="navigation">
|
|
108 <li class="header-nav-item">
|
|
109 <a href="/pulls" class="js-selected-navigation-item header-nav-link" data-ga-click="Header, click, Nav menu - item:pulls context:user" data-hotkey="g p" data-selected-links="/pulls /pulls/assigned /pulls/mentioned /pulls">
|
|
110 Pull requests
|
|
111 </a> </li>
|
|
112 <li class="header-nav-item">
|
|
113 <a href="/issues" class="js-selected-navigation-item header-nav-link" data-ga-click="Header, click, Nav menu - item:issues context:user" data-hotkey="g i" data-selected-links="/issues /issues/assigned /issues/mentioned /issues">
|
|
114 Issues
|
|
115 </a> </li>
|
|
116 <li class="header-nav-item">
|
|
117 <a class="header-nav-link" href="https://gist.github.com/" data-ga-click="Header, go to gist, text:gist">Gist</a>
|
|
118 </li>
|
|
119 </ul>
|
|
120
|
|
121
|
|
122 <ul class="header-nav user-nav right" id="user-links">
|
|
123 <li class="header-nav-item">
|
|
124 <span class="js-socket-channel js-updatable-content"
|
|
125 data-channel="notification-changed:Eduardo-Alves"
|
|
126 data-url="/notifications/header">
|
|
127 <a href="/notifications" aria-label="You have no unread notifications" class="header-nav-link notification-indicator tooltipped tooltipped-s" data-ga-click="Header, go to notifications, icon:read" data-hotkey="g n">
|
|
128 <span class="mail-status all-read"></span>
|
|
129 <span class="octicon octicon-inbox"></span>
|
|
130 </a> </span>
|
|
131
|
|
132 </li>
|
|
133
|
|
134 <li class="header-nav-item dropdown js-menu-container">
|
|
135 <a class="header-nav-link tooltipped tooltipped-s js-menu-target" href="/new"
|
|
136 aria-label="Create newโฆ"
|
|
137 data-ga-click="Header, create new, icon:add">
|
|
138 <span class="octicon octicon-plus left"></span>
|
|
139 <span class="dropdown-caret"></span>
|
|
140 </a>
|
|
141
|
|
142 <div class="dropdown-menu-content js-menu-content">
|
|
143 <ul class="dropdown-menu dropdown-menu-sw">
|
|
144
|
|
145 <a class="dropdown-item" href="/new" data-ga-click="Header, create new repository">
|
|
146 New repository
|
|
147 </a>
|
|
148
|
|
149
|
|
150 <a class="dropdown-item" href="/organizations/new" data-ga-click="Header, create new organization">
|
|
151 New organization
|
|
152 </a>
|
|
153
|
|
154
|
|
155
|
|
156 <div class="dropdown-divider"></div>
|
|
157 <div class="dropdown-header">
|
|
158 <span title="galaxyproject/tools-devteam">This repository</span>
|
|
159 </div>
|
|
160 <a class="dropdown-item" href="/galaxyproject/tools-devteam/issues/new" data-ga-click="Header, create new issue">
|
|
161 New issue
|
|
162 </a>
|
|
163
|
|
164 </ul>
|
|
165 </div>
|
|
166 </li>
|
|
167
|
|
168 <li class="header-nav-item dropdown js-menu-container">
|
|
169 <a class="header-nav-link name tooltipped tooltipped-s js-menu-target" href="/Eduardo-Alves"
|
|
170 aria-label="View profile and more"
|
|
171 data-ga-click="Header, show menu, icon:avatar">
|
|
172 <img alt="@Eduardo-Alves" class="avatar" height="20" src="https://avatars1.githubusercontent.com/u/9776977?v=3&s=40" width="20" />
|
|
173 <span class="dropdown-caret"></span>
|
|
174 </a>
|
|
175
|
|
176 <div class="dropdown-menu-content js-menu-content">
|
|
177 <div class="dropdown-menu dropdown-menu-sw">
|
|
178 <div class="dropdown-header header-nav-current-user css-truncate">
|
|
179 Signed in as <strong class="css-truncate-target">Eduardo-Alves</strong>
|
|
180 </div>
|
|
181 <div class="dropdown-divider"></div>
|
|
182
|
|
183 <a class="dropdown-item" href="/Eduardo-Alves" data-ga-click="Header, go to profile, text:your profile">
|
|
184 Your profile
|
|
185 </a>
|
|
186 <a class="dropdown-item" href="/stars" data-ga-click="Header, go to starred repos, text:your stars">
|
|
187 Your stars
|
|
188 </a>
|
|
189 <a class="dropdown-item" href="/explore" data-ga-click="Header, go to explore, text:explore">
|
|
190 Explore
|
|
191 </a>
|
|
192 <a class="dropdown-item" href="https://help.github.com" data-ga-click="Header, go to help, text:help">
|
|
193 Help
|
|
194 </a>
|
|
195 <div class="dropdown-divider"></div>
|
|
196
|
|
197 <a class="dropdown-item" href="/settings/profile" data-ga-click="Header, go to settings, icon:settings">
|
|
198 Settings
|
|
199 </a>
|
|
200
|
|
201 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/logout" class="logout-form" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="fMiuMnZEhOyhrkDmQMsMGi4+rgqhqa/5AyAG+2bEQj/sNUfzQZ3FUFyIjO15HQuxl0IIXgOxpQ+/rGZ4GamDuA==" /></div>
|
|
202 <button class="dropdown-item dropdown-signout" data-ga-click="Header, sign out, icon:logout">
|
|
203 Sign out
|
|
204 </button>
|
|
205 </form> </div>
|
|
206 </div>
|
|
207 </li>
|
|
208 </ul>
|
|
209
|
|
210
|
|
211
|
|
212 </div>
|
|
213 </div>
|
|
214
|
|
215
|
|
216
|
|
217
|
|
218
|
|
219
|
|
220 <div id="start-of-content" class="accessibility-aid"></div>
|
|
221 <div class="site" itemscope itemtype="http://schema.org/WebPage">
|
|
222 <div id="js-flash-container">
|
|
223
|
|
224 </div>
|
|
225 <div class="pagehead repohead instapaper_ignore readability-menu ">
|
|
226 <div class="container">
|
|
227
|
|
228 <div class="clearfix">
|
|
229
|
|
230 <ul class="pagehead-actions">
|
|
231
|
|
232 <li>
|
|
233 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="DGdw+xCuQFxtIYNwCNm6pBV1JG27b3WKuUifr1dYxp0y2kRvMyTGOVGs0z/mJP2iVSvhaoCMK/7UQID8gHh2Bg==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="24609401" />
|
|
234
|
|
235 <div class="select-menu js-menu-container js-select-menu">
|
|
236 <a href="/galaxyproject/tools-devteam/subscription"
|
|
237 class="btn btn-sm btn-with-count select-menu-button js-menu-target" role="button" tabindex="0" aria-haspopup="true"
|
|
238 data-ga-click="Repository, click Watch settings, action:files#disambiguate">
|
|
239 <span class="js-select-button">
|
|
240 <span class="octicon octicon-eye"></span>
|
|
241 Watch
|
|
242 </span>
|
|
243 </a>
|
|
244 <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/watchers">
|
|
245 24
|
|
246 </a>
|
|
247
|
|
248 <div class="select-menu-modal-holder">
|
|
249 <div class="select-menu-modal subscription-menu-modal js-menu-content" aria-hidden="true">
|
|
250 <div class="select-menu-header">
|
|
251 <span class="select-menu-title">Notifications</span>
|
|
252 <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
|
|
253 </div>
|
|
254
|
|
255 <div class="select-menu-list js-navigation-container" role="menu">
|
|
256
|
|
257 <div class="select-menu-item js-navigation-item selected" role="menuitem" tabindex="0">
|
|
258 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
259 <div class="select-menu-item-text">
|
|
260 <input checked="checked" id="do_included" name="do" type="radio" value="included" />
|
|
261 <span class="select-menu-item-heading">Not watching</span>
|
|
262 <span class="description">Be notified when participating or @mentioned.</span>
|
|
263 <span class="js-select-button-text hidden-select-button-text">
|
|
264 <span class="octicon octicon-eye"></span>
|
|
265 Watch
|
|
266 </span>
|
|
267 </div>
|
|
268 </div>
|
|
269
|
|
270 <div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0">
|
|
271 <span class="select-menu-item-icon octicon octicon octicon-check"></span>
|
|
272 <div class="select-menu-item-text">
|
|
273 <input id="do_subscribed" name="do" type="radio" value="subscribed" />
|
|
274 <span class="select-menu-item-heading">Watching</span>
|
|
275 <span class="description">Be notified of all conversations.</span>
|
|
276 <span class="js-select-button-text hidden-select-button-text">
|
|
277 <span class="octicon octicon-eye"></span>
|
|
278 Unwatch
|
|
279 </span>
|
|
280 </div>
|
|
281 </div>
|
|
282
|
|
283 <div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0">
|
|
284 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
285 <div class="select-menu-item-text">
|
|
286 <input id="do_ignore" name="do" type="radio" value="ignore" />
|
|
287 <span class="select-menu-item-heading">Ignoring</span>
|
|
288 <span class="description">Never be notified.</span>
|
|
289 <span class="js-select-button-text hidden-select-button-text">
|
|
290 <span class="octicon octicon-mute"></span>
|
|
291 Stop ignoring
|
|
292 </span>
|
|
293 </div>
|
|
294 </div>
|
|
295
|
|
296 </div>
|
|
297
|
|
298 </div>
|
|
299 </div>
|
|
300 </div>
|
|
301 </form>
|
|
302 </li>
|
|
303
|
|
304 <li>
|
|
305
|
|
306 <div class="js-toggler-container js-social-container starring-container ">
|
|
307
|
|
308 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/galaxyproject/tools-devteam/unstar" class="js-toggler-form starred js-unstar-button" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="Ht42QwygpPl/X73KcFLmQCxxcdx/1y0l14CZTEHW2Vq26NXTPZeJzB75rLW1E8MCfjNx8kM/gtL7Bj++i42Hqw==" /></div>
|
|
309 <button
|
|
310 class="btn btn-sm btn-with-count js-toggler-target"
|
|
311 aria-label="Unstar this repository" title="Unstar galaxyproject/tools-devteam"
|
|
312 data-ga-click="Repository, click unstar button, action:files#disambiguate; text:Unstar">
|
|
313 <span class="octicon octicon-star"></span>
|
|
314 Unstar
|
|
315 </button>
|
|
316 <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/stargazers">
|
|
317 19
|
|
318 </a>
|
|
319 </form>
|
|
320 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/galaxyproject/tools-devteam/star" class="js-toggler-form unstarred js-star-button" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="6+bTm7HvK1uJumzv5UnNLmaxSsU8iay+YbSTHv1POclPVy0/pZ8dGEFa6KSydr5IODuKFDPDUWfT1CVZohJWbg==" /></div>
|
|
321 <button
|
|
322 class="btn btn-sm btn-with-count js-toggler-target"
|
|
323 aria-label="Star this repository" title="Star galaxyproject/tools-devteam"
|
|
324 data-ga-click="Repository, click star button, action:files#disambiguate; text:Star">
|
|
325 <span class="octicon octicon-star"></span>
|
|
326 Star
|
|
327 </button>
|
|
328 <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/stargazers">
|
|
329 19
|
|
330 </a>
|
|
331 </form> </div>
|
|
332
|
|
333 </li>
|
|
334
|
|
335 <li>
|
|
336 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/galaxyproject/tools-devteam/fork" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="H1FuVDtgFQPJa4u54gOwTwCDWCBI04EQxSKX0K0kKthHk+HCt7jO65YZ06gha5KaohunsXkE+Fi0GqqEXx3ruA==" /></div>
|
|
337 <button
|
|
338 type="submit"
|
|
339 class="btn btn-sm btn-with-count"
|
|
340 data-ga-click="Repository, show fork modal, action:files#disambiguate; text:Fork"
|
|
341 title="Fork your own copy of galaxyproject/tools-devteam to your account"
|
|
342 aria-label="Fork your own copy of galaxyproject/tools-devteam to your account">
|
|
343 <span class="octicon octicon-repo-forked"></span>
|
|
344 Fork
|
|
345 </button>
|
|
346 <a href="/galaxyproject/tools-devteam/network" class="social-count">32</a>
|
|
347 </form> </li>
|
|
348
|
|
349 </ul>
|
|
350
|
|
351 <h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public ">
|
|
352 <span class="mega-octicon octicon-repo"></span>
|
|
353 <span class="author"><a href="/galaxyproject" class="url fn" itemprop="url" rel="author"><span itemprop="title">galaxyproject</span></a></span><!--
|
|
354 --><span class="path-divider">/</span><!--
|
|
355 --><strong><a href="/galaxyproject/tools-devteam" data-pjax="#js-repo-pjax-container">tools-devteam</a></strong>
|
|
356
|
|
357 <span class="page-context-loader">
|
|
358 <img alt="" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
359 </span>
|
|
360
|
|
361 </h1>
|
|
362 </div>
|
|
363
|
|
364 </div>
|
|
365 </div>
|
|
366
|
|
367 <div class="container">
|
|
368 <div class="repository-with-sidebar repo-container new-discussion-timeline ">
|
|
369 <div class="repository-sidebar clearfix">
|
|
370
|
|
371
|
|
372 <nav class="sunken-menu repo-nav js-repo-nav js-sidenav-container-pjax js-octicon-loaders"
|
|
373 role="navigation"
|
|
374 data-pjax="#js-repo-pjax-container"
|
|
375 data-issue-count-url="/galaxyproject/tools-devteam/issues/counts">
|
|
376 <ul class="sunken-menu-group">
|
|
377 <li class="tooltipped tooltipped-w" aria-label="Code">
|
|
378 <a href="/galaxyproject/tools-devteam" aria-label="Code" aria-selected="true" class="js-selected-navigation-item selected sunken-menu-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /galaxyproject/tools-devteam">
|
|
379 <span class="octicon octicon-code"></span> <span class="full-word">Code</span>
|
|
380 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
381 </a> </li>
|
|
382
|
|
383 <li class="tooltipped tooltipped-w" aria-label="Issues">
|
|
384 <a href="/galaxyproject/tools-devteam/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 /galaxyproject/tools-devteam/issues">
|
|
385 <span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span>
|
|
386 <span class="js-issue-replace-counter"></span>
|
|
387 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
388 </a> </li>
|
|
389
|
|
390 <li class="tooltipped tooltipped-w" aria-label="Pull requests">
|
|
391 <a href="/galaxyproject/tools-devteam/pulls" aria-label="Pull requests" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g p" data-selected-links="repo_pulls /galaxyproject/tools-devteam/pulls">
|
|
392 <span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull requests</span>
|
|
393 <span class="js-pull-replace-counter"></span>
|
|
394 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
395 </a> </li>
|
|
396
|
|
397 <li class="tooltipped tooltipped-w" aria-label="Wiki">
|
|
398 <a href="/galaxyproject/tools-devteam/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g w" data-selected-links="repo_wiki /galaxyproject/tools-devteam/wiki">
|
|
399 <span class="octicon octicon-book"></span> <span class="full-word">Wiki</span>
|
|
400 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
401 </a> </li>
|
|
402 </ul>
|
|
403 <div class="sunken-menu-separator"></div>
|
|
404 <ul class="sunken-menu-group">
|
|
405
|
|
406 <li class="tooltipped tooltipped-w" aria-label="Pulse">
|
|
407 <a href="/galaxyproject/tools-devteam/pulse" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-selected-links="pulse /galaxyproject/tools-devteam/pulse">
|
|
408 <span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span>
|
|
409 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
410 </a> </li>
|
|
411
|
|
412 <li class="tooltipped tooltipped-w" aria-label="Graphs">
|
|
413 <a href="/galaxyproject/tools-devteam/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-selected-links="repo_graphs repo_contributors /galaxyproject/tools-devteam/graphs">
|
|
414 <span class="octicon octicon-graph"></span> <span class="full-word">Graphs</span>
|
|
415 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
416 </a> </li>
|
|
417 </ul>
|
|
418
|
|
419
|
|
420 </nav>
|
|
421
|
|
422 <div class="only-with-full-nav">
|
|
423
|
|
424 <div class="js-clone-url clone-url open"
|
|
425 data-protocol-type="http">
|
|
426 <h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
|
|
427 <div class="input-group js-zeroclipboard-container">
|
|
428 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
429 value="https://github.com/galaxyproject/tools-devteam.git" readonly="readonly" aria-label="HTTPS clone URL">
|
|
430 <span class="input-group-button">
|
|
431 <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>
|
|
432 </span>
|
|
433 </div>
|
|
434 </div>
|
|
435
|
|
436
|
|
437 <div class="js-clone-url clone-url "
|
|
438 data-protocol-type="ssh">
|
|
439 <h3><span class="text-emphasized">SSH</span> clone URL</h3>
|
|
440 <div class="input-group js-zeroclipboard-container">
|
|
441 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
442 value="git@github.com:galaxyproject/tools-devteam.git" readonly="readonly" aria-label="SSH clone URL">
|
|
443 <span class="input-group-button">
|
|
444 <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>
|
|
445 </span>
|
|
446 </div>
|
|
447 </div>
|
|
448
|
|
449
|
|
450 <div class="js-clone-url clone-url "
|
|
451 data-protocol-type="subversion">
|
|
452 <h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
|
|
453 <div class="input-group js-zeroclipboard-container">
|
|
454 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
|
|
455 value="https://github.com/galaxyproject/tools-devteam" readonly="readonly" aria-label="Subversion checkout URL">
|
|
456 <span class="input-group-button">
|
|
457 <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>
|
|
458 </span>
|
|
459 </div>
|
|
460 </div>
|
|
461
|
|
462
|
|
463
|
|
464 <div class="clone-options">You can clone with
|
|
465 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/users/set_protocol?protocol_selector=http&protocol_type=clone" class="inline-form js-clone-selector-form is-enabled" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="p0VQsIljGBrHndcjPpG9Dpq4dU5QLFyPkE10kEIE2Bktu6AqKJYq5czMBGsNq9+NATbCDeeRGSQunprJjDO//w==" /></div><button class="btn-link js-clone-selector" data-protocol="http" type="submit">HTTPS</button></form>, <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/users/set_protocol?protocol_selector=ssh&protocol_type=clone" class="inline-form js-clone-selector-form is-enabled" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="y1gtOi4F0/sEcx8I6AzpiNaNbqfOyhYdpAnwK8y0D1WSZtbyxL7EXbfpe/9ZrKzKr8StSTFzsivAM2dIgTpcfg==" /></div><button class="btn-link js-clone-selector" data-protocol="ssh" type="submit">SSH</button></form>, or <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/users/set_protocol?protocol_selector=subversion&protocol_type=clone" class="inline-form js-clone-selector-form is-enabled" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="5gZ3Tjopo59VHlYso40Bnv7gWAcX9rxMsdmVeuNVKJl+6c/ihs0Wa4/t4IjSYbaRGqAKez0tmMfsVleU3w95KA==" /></div><button class="btn-link js-clone-selector" data-protocol="subversion" type="submit">Subversion</button></form>.
|
|
466 <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.">
|
|
467 <span class="octicon octicon-question"></span>
|
|
468 </a>
|
|
469 </div>
|
|
470
|
|
471 <a href="/galaxyproject/tools-devteam/archive/master.zip"
|
|
472 class="btn btn-sm sidebar-button"
|
|
473 aria-label="Download the contents of galaxyproject/tools-devteam as a zip file"
|
|
474 title="Download the contents of galaxyproject/tools-devteam as a zip file"
|
|
475 rel="nofollow">
|
|
476 <span class="octicon octicon-cloud-download"></span>
|
|
477 Download ZIP
|
|
478 </a>
|
|
479 </div>
|
|
480 </div>
|
|
481 <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container>
|
|
482
|
|
483
|
|
484 <div class="file-navigation">
|
|
485
|
|
486 <div class="select-menu js-menu-container js-select-menu left">
|
|
487 <span class="btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w"
|
|
488 data-ref="master"
|
|
489 title="master"
|
|
490 role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true">
|
|
491 <i>Branch:</i>
|
|
492 <span class="js-select-button css-truncate-target">master</span>
|
|
493 </span>
|
|
494
|
|
495 <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true">
|
|
496
|
|
497 <div class="select-menu-modal">
|
|
498 <div class="select-menu-header">
|
|
499 <span class="select-menu-title">Switch branches/tags</span>
|
|
500 <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
|
|
501 </div>
|
|
502
|
|
503 <div class="select-menu-filters">
|
|
504 <div class="select-menu-text-filter">
|
|
505 <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags">
|
|
506 </div>
|
|
507 <div class="select-menu-tabs">
|
|
508 <ul>
|
|
509 <li class="select-menu-tab">
|
|
510 <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a>
|
|
511 </li>
|
|
512 <li class="select-menu-tab">
|
|
513 <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tagโฆ" class="js-select-menu-tab" role="tab">Tags</a>
|
|
514 </li>
|
|
515 </ul>
|
|
516 </div>
|
|
517 </div>
|
|
518
|
|
519 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu">
|
|
520
|
|
521 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
|
|
522
|
|
523
|
|
524 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
525 href="/galaxyproject/tools-devteam/tree/bamtools/tools/bowtie2/test-data"
|
|
526 data-name="bamtools"
|
|
527 data-skip-pjax="true"
|
|
528 rel="nofollow">
|
|
529 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
530 <span class="select-menu-item-text css-truncate-target" title="bamtools">
|
|
531 bamtools
|
|
532 </span>
|
|
533 </a>
|
|
534 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
535 href="/galaxyproject/tools-devteam/tree/bamtools_images/tools/bowtie2/test-data"
|
|
536 data-name="bamtools_images"
|
|
537 data-skip-pjax="true"
|
|
538 rel="nofollow">
|
|
539 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
540 <span class="select-menu-item-text css-truncate-target" title="bamtools_images">
|
|
541 bamtools_images
|
|
542 </span>
|
|
543 </a>
|
|
544 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
545 href="/galaxyproject/tools-devteam/tree/blankenberg-dm-samtools-fix-1/tools/bowtie2/test-data"
|
|
546 data-name="blankenberg-dm-samtools-fix-1"
|
|
547 data-skip-pjax="true"
|
|
548 rel="nofollow">
|
|
549 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
550 <span class="select-menu-item-text css-truncate-target" title="blankenberg-dm-samtools-fix-1">
|
|
551 blankenberg-dm-samtools-fix-1
|
|
552 </span>
|
|
553 </a>
|
|
554 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
555 href="/galaxyproject/tools-devteam/tree/hisat/tools/bowtie2/test-data"
|
|
556 data-name="hisat"
|
|
557 data-skip-pjax="true"
|
|
558 rel="nofollow">
|
|
559 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
560 <span class="select-menu-item-text css-truncate-target" title="hisat">
|
|
561 hisat
|
|
562 </span>
|
|
563 </a>
|
|
564 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
565 href="/galaxyproject/tools-devteam/tree/libgd-export/tools/bowtie2/test-data"
|
|
566 data-name="libgd-export"
|
|
567 data-skip-pjax="true"
|
|
568 rel="nofollow">
|
|
569 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
570 <span class="select-menu-item-text css-truncate-target" title="libgd-export">
|
|
571 libgd-export
|
|
572 </span>
|
|
573 </a>
|
|
574 <a class="select-menu-item js-navigation-item js-navigation-open selected"
|
|
575 href="/galaxyproject/tools-devteam/tree/master/tools/bowtie2/test-data"
|
|
576 data-name="master"
|
|
577 data-skip-pjax="true"
|
|
578 rel="nofollow">
|
|
579 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
580 <span class="select-menu-item-text css-truncate-target" title="master">
|
|
581 master
|
|
582 </span>
|
|
583 </a>
|
|
584 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
585 href="/galaxyproject/tools-devteam/tree/origin/hisat/tools/bowtie2/test-data"
|
|
586 data-name="origin/hisat"
|
|
587 data-skip-pjax="true"
|
|
588 rel="nofollow">
|
|
589 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
590 <span class="select-menu-item-text css-truncate-target" title="origin/hisat">
|
|
591 origin/hisat
|
|
592 </span>
|
|
593 </a>
|
|
594 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
595 href="/galaxyproject/tools-devteam/tree/osx_compat/tools/bowtie2/test-data"
|
|
596 data-name="osx_compat"
|
|
597 data-skip-pjax="true"
|
|
598 rel="nofollow">
|
|
599 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
600 <span class="select-menu-item-text css-truncate-target" title="osx_compat">
|
|
601 osx_compat
|
|
602 </span>
|
|
603 </a>
|
|
604 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
605 href="/galaxyproject/tools-devteam/tree/picard_sortsam/tools/bowtie2/test-data"
|
|
606 data-name="picard_sortsam"
|
|
607 data-skip-pjax="true"
|
|
608 rel="nofollow">
|
|
609 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
610 <span class="select-menu-item-text css-truncate-target" title="picard_sortsam">
|
|
611 picard_sortsam
|
|
612 </span>
|
|
613 </a>
|
|
614 <a class="select-menu-item js-navigation-item js-navigation-open "
|
|
615 href="/galaxyproject/tools-devteam/tree/weblogo-fix/tools/bowtie2/test-data"
|
|
616 data-name="weblogo-fix"
|
|
617 data-skip-pjax="true"
|
|
618 rel="nofollow">
|
|
619 <span class="select-menu-item-icon octicon octicon-check"></span>
|
|
620 <span class="select-menu-item-text css-truncate-target" title="weblogo-fix">
|
|
621 weblogo-fix
|
|
622 </span>
|
|
623 </a>
|
|
624 </div>
|
|
625
|
|
626 <div class="select-menu-no-results">Nothing to show</div>
|
|
627 </div>
|
|
628
|
|
629 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags">
|
|
630 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
|
|
631
|
|
632
|
|
633 </div>
|
|
634
|
|
635 <div class="select-menu-no-results">Nothing to show</div>
|
|
636 </div>
|
|
637
|
|
638 </div>
|
|
639 </div>
|
|
640 </div>
|
|
641
|
|
642 <div class="btn-group right">
|
|
643 <a href="/galaxyproject/tools-devteam/find/master" data-pjax data-hotkey="t" class="js-show-file-finder btn btn-sm empty-icon tooltipped tooltipped-s" aria-label="Quickly jump between files">
|
|
644 <span class="octicon octicon-list-unordered"></span>
|
|
645 </a>
|
|
646 <a href="/galaxyproject/tools-devteam/commits/master/tools/bowtie2/test-data" class="btn btn-sm empty-icon tooltipped tooltipped-s" aria-label="Browse commits for this branch">
|
|
647 <span class="octicon octicon-history"></span>
|
|
648 </a>
|
|
649 </div>
|
|
650 <div class="breadcrumb">
|
|
651 <span class="repo-root js-repo-root"><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/galaxyproject/tools-devteam" class="" data-branch="master" data-pjax="true" itemscope="url"><span itemprop="title">tools-devteam</span></a></span></span><span class="separator">/</span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/galaxyproject/tools-devteam/tree/master/tools" class="" data-branch="master" data-pjax="true" itemscope="url"><span itemprop="title">tools</span></a></span><span class="separator">/</span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/galaxyproject/tools-devteam/tree/master/tools/bowtie2" class="" data-branch="master" data-pjax="true" itemscope="url"><span itemprop="title">bowtie2</span></a></span><span class="separator">/</span><strong class="final-path">test-data</strong><span class="separator">/</span>
|
|
652 <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/galaxyproject/tools-devteam/new/master/tools/bowtie2/test-data" class="js-new-blob-form inline-form" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="oHnhBUKtIFc/i+gj1F8SdSSK6r2vwLo0csLvt6huBR6W4GyuyAl915tvYyDR2eLrs8hxzyu3b0Ooq8FsVZjYww==" /></div>
|
|
653 <button class="btn-link tooltipped tooltipped-e" type="submit" data-disable-with="workingโฆ" aria-label="Fork this project and create a new file">
|
|
654 <span class="js-new-blob-submit octicon octicon-plus"></span>
|
|
655 </button>
|
|
656 </form>
|
|
657 </div>
|
|
658 </div>
|
|
659
|
|
660
|
|
661
|
|
662
|
|
663 <div class="commit commit-tease js-details-container" >
|
|
664 <p class="commit-title ">
|
|
665 <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling.
|
|
666
|
|
667 The reusable macro file has:
|
|
668
|
|
669 - Defines widgets for common read group parameters.
|
|
670 - Widgets can be used at top-level (e.g. ``picard_AddOrReplaceReadGroups`` where handling is required) of inputs or within a conditional (e.g. in the mappers).
|
|
671 - The conditional (used by mappers) has fours modes:
|
|
672 - Set according the specification (only ID required - has all parameters). Current BWA approach.
|
|
673 - Set Picard-style (presumably useful for broad pipelines?) (``ID``, ``SM``, ``LB``, ``PU``, ``PL`` are all required and there are no params for ``KS``, ``PG``, or ``FO``). In terms of what is shown and what is required - this mirrors ``picard_AddOrReplaceReadGroups``.
|
|
674 - Just assign the ``ID`` and do so automatically (based either on collection or standalone dataset information). No extra form elements are shown to the user. (Should this be the new default?)
|
|
675 - Do not set read groups.
|
|
676 - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance).
|
|
677 - An example "mapper" test tool which demonstrates optionally including read groups.
|
|
678 - An example read group assign test tool which demonstrates unconditionally specifying macros.
|
|
679
|
|
680 In addition to unifying everything, the macro file defines enhanced ``ID``, ``SM``, and ``LB`` parameter inputs that are wrapped in a conditional. That conditional allows manual input but also allows the user to just say Galaxy should use collection information or dataset name (if input is not in a collection) to assign these parameters. This should simplify things and make simple workflows more robust, but is absolutely essential for collection-based workflows and newer tool form options that allow running a tool in parallel over many inputs.
|
|
681
|
|
682 This may look at first glance like it is really complicated - but if you focus just on the mappers for instance and treat the macro file like a library - the client interface is actually a good deal easier than doing this stuff by hand for each tool.
|
|
683
|
|
684 Updates from original version:
|
|
685
|
|
686 - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools.
|
|
687 - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments).
|
|
688 - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that).
|
|
689
|
|
690 Smaller Notes:
|
|
691
|
|
692 The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine:
|
|
693
|
|
694 ```
|
|
695 -@RG ID:rg1 SM: PL:CAPILLARY
|
|
696 -@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 SM: PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpn_I5mQ/files/000/dataset_9.dat /tmp/tmpn_I5mQ/files/000/dataset_10.dat
|
|
697 +@RG ID:rg1 PL:CAPILLARY
|
|
698 +@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpmN3j1j/files/000/dataset_9.dat /tmp/tmpmN3j1j/files/000/dataset_10.dat
|
|
699 ```">Unify and collectionify read group handling.</a>
|
|
700 <span class="hidden-text-expander inline"><a href="#" class="js-details-target">โฆ</a></span>
|
|
701 </p>
|
|
702 <div class="commit-desc"><pre>The reusable macro file has:
|
|
703
|
|
704 - Defines widgets for common read group parameters.
|
|
705 - Widgets can be used at top-level (e.g. ``picard_AddOrReplaceReadGroups`` where handling is required) of inputs or within a conditional (e.g. in the mappers).
|
|
706 - The conditional (used by mappers) has fours modes:
|
|
707 - Set according the specification (only ID required - has all parameters). Current BWA approach.
|
|
708 - Set Picard-style (presumably useful for broad pipelines?) (``ID``, ``SM``, ``LB``, ``PU``, ``PL`` are all required and there are no params for ``KS``, ``PG``, or ``FO``). In terms of what is shown and what is required - this mirrors ``picard_AddOrReplaceReadGroups``.
|
|
709 - Just assign the ``ID`` and do so automatically (based either on collection or standalone dataset information). No extra form elements are shown to the user. (Should this be the new default?)
|
|
710 - Do not set read groups.
|
|
711 - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance).
|
|
712 - An example "mapper" test tool which demonstrates optionally including read groups.
|
|
713 - An example read group assign test tool which demonstrates unconditionally specifying macros.
|
|
714
|
|
715 In addition to unifying everything, the macro file defines enhanced ``ID``, ``SM``, and ``LB`` parameter inputs that are wrapped in a conditional. That conditional allows manual input but also allows the user to just say Galaxy should use collection information or dataset name (if input is not in a collection) to assign these parameters. This should simplify things and make simple workflows more robust, but is absolutely essential for collection-based workflows and newer tool form options that allow running a tool in parallel over many inputs.
|
|
716
|
|
717 This may look at first glance like it is really complicated - but if you focus just on the mappers for instance and treat the macro file like a library - the client interface is actually a good deal easier than doing this stuff by hand for each tool.
|
|
718
|
|
719 Updates from original version:
|
|
720
|
|
721 - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools.
|
|
722 - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments).
|
|
723 - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that).
|
|
724
|
|
725 Smaller Notes:
|
|
726
|
|
727 The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine:
|
|
728
|
|
729 ```
|
|
730 -<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 SM: PL:CAPILLARY
|
|
731 -<a href="https://github.com/PG" class="user-mention">@PG</a> ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r <a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 SM: PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpn_I5mQ/files/000/dataset_9.dat /tmp/tmpn_I5mQ/files/000/dataset_10.dat
|
|
732 +<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 PL:CAPILLARY
|
|
733 +<a href="https://github.com/PG" class="user-mention">@PG</a> ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r <a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpmN3j1j/files/000/dataset_9.dat /tmp/tmpmN3j1j/files/000/dataset_10.dat
|
|
734 ```</pre></div>
|
|
735 <div class="commit-meta">
|
|
736 <button aria-label="Copy SHA" class="js-zeroclipboard zeroclipboard-link tooltipped tooltipped-s" data-clipboard-text="d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
|
|
737 <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="sha-block" data-pjax>latest commit <span class="sha">d0e3412c58</span></a>
|
|
738
|
|
739 <div class="authorship">
|
|
740 <img alt="@jmchilton" class="avatar" height="20" src="https://avatars0.githubusercontent.com/u/216771?v=3&s=40" width="20" />
|
|
741 <span class="author-name"><a href="/jmchilton" rel="contributor">jmchilton</a></span>
|
|
742 authored <time class="updated" datetime="2015-04-13T20:08:40Z" is="relative-time">Apr 13, 2015</time>
|
|
743
|
|
744 </div>
|
|
745 </div>
|
|
746 </div>
|
|
747
|
|
748
|
|
749 <div class="file-wrap">
|
|
750 <a href="/galaxyproject/tools-devteam/tree/22227a626113448672603f832bdccba36dd3fdac/tools/bowtie2/test-data" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a>
|
|
751
|
|
752 <table class="files" data-pjax>
|
|
753 <tr class="up-tree">
|
|
754 <td></td>
|
|
755 <td><a href="/galaxyproject/tools-devteam/tree/master/tools/bowtie2" rel="nofollow" title="Go to parent directory">..</a></td>
|
|
756 <td></td>
|
|
757 <td></td>
|
|
758 </tr>
|
|
759
|
|
760
|
|
761 <tbody>
|
|
762 <tr class="warning include-fragment-error">
|
|
763 <td class="icon"><span class="octicon octicon-alert"></span></td>
|
|
764 <td class="content" colspan="3">Failed to load latest commit information.</td>
|
|
765 </tr>
|
|
766
|
|
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/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
771 </td>
|
|
772 <td class="content">
|
|
773 <span class="css-truncate css-truncate-target"><a href="/galaxyproject/tools-devteam/blob/master/tools/bowtie2/test-data/bowtie2-fq1.fq" class="js-directory-link" id="be347569b1fed463c3e111292bc2df9e-fa44b3385f96a1913c84e2a5b3f01d323195eb94" title="bowtie2-fq1.fq">bowtie2-fq1.fq</a></span>
|
|
774 </td>
|
|
775 <td class="message">
|
|
776 <span class="css-truncate css-truncate-target">
|
|
777 <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a>
|
|
778 </span>
|
|
779 </td>
|
|
780 <td class="age">
|
|
781 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
|
|
782 </td>
|
|
783 </tr>
|
|
784 <tr>
|
|
785 <td class="icon">
|
|
786 <span class="octicon octicon-file-text"></span>
|
|
787 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
788 </td>
|
|
789 <td class="content">
|
|
790 <span class="css-truncate css-truncate-target"><a href="/galaxyproject/tools-devteam/blob/master/tools/bowtie2/test-data/bowtie2-fq2.fq" class="js-directory-link" id="a93db4f1ea9cdfa0f62c8f46bd3aed01-ff3c56bb5eeef08c79e0c5a774aa521d9ff23ac4" title="bowtie2-fq2.fq">bowtie2-fq2.fq</a></span>
|
|
791 </td>
|
|
792 <td class="message">
|
|
793 <span class="css-truncate css-truncate-target">
|
|
794 <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a>
|
|
795 </span>
|
|
796 </td>
|
|
797 <td class="age">
|
|
798 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
|
|
799 </td>
|
|
800 </tr>
|
|
801 <tr>
|
|
802 <td class="icon">
|
|
803 <span class="octicon octicon-file-text"></span>
|
|
804 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
805 </td>
|
|
806 <td class="content">
|
|
807 <span class="css-truncate css-truncate-target"><a href="/galaxyproject/tools-devteam/blob/master/tools/bowtie2/test-data/bowtie2-ref.fasta" class="js-directory-link" id="fe1438a7ee4d5e5f4d293552666ee44a-a4b24136e8e93939311f3c345110ba6abe91d36c" title="bowtie2-ref.fasta">bowtie2-ref.fasta</a></span>
|
|
808 </td>
|
|
809 <td class="message">
|
|
810 <span class="css-truncate css-truncate-target">
|
|
811 <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a>
|
|
812 </span>
|
|
813 </td>
|
|
814 <td class="age">
|
|
815 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
|
|
816 </td>
|
|
817 </tr>
|
|
818 <tr>
|
|
819 <td class="icon">
|
|
820 <span class="octicon octicon-file-text"></span>
|
|
821 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
822 </td>
|
|
823 <td class="content">
|
|
824 <span class="css-truncate css-truncate-target"><a href="/galaxyproject/tools-devteam/blob/master/tools/bowtie2/test-data/bowtie2-test1.bam" class="js-directory-link" id="ef319980eaff46c21c428e7b81e28236-e23d7aef9ed985714347793a92b674b449ec8fe3" title="bowtie2-test1.bam">bowtie2-test1.bam</a></span>
|
|
825 </td>
|
|
826 <td class="message">
|
|
827 <span class="css-truncate css-truncate-target">
|
|
828 <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a>
|
|
829 </span>
|
|
830 </td>
|
|
831 <td class="age">
|
|
832 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
|
|
833 </td>
|
|
834 </tr>
|
|
835 <tr>
|
|
836 <td class="icon">
|
|
837 <span class="octicon octicon-file-text"></span>
|
|
838 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
|
|
839 </td>
|
|
840 <td class="content">
|
|
841 <span class="css-truncate css-truncate-target"><a href="/galaxyproject/tools-devteam/blob/master/tools/bowtie2/test-data/bowtie2-test2.bam" class="js-directory-link" id="fcef5de0c5311dd568ad01705dfbcf96-12df83659d247d24c2a6dbb51740559bc73643b9" title="bowtie2-test2.bam">bowtie2-test2.bam</a></span>
|
|
842 </td>
|
|
843 <td class="message">
|
|
844 <span class="css-truncate css-truncate-target">
|
|
845 <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling.
|
|
846
|
|
847 The reusable macro file has:
|
|
848
|
|
849 - Defines widgets for common read group parameters.
|
|
850 - Widgets can be used at top-level (e.g. ``picard_AddOrReplaceReadGroups`` where handling is required) of inputs or within a conditional (e.g. in the mappers).
|
|
851 - The conditional (used by mappers) has fours modes:
|
|
852 - Set according the specification (only ID required - has all parameters). Current BWA approach.
|
|
853 - Set Picard-style (presumably useful for broad pipelines?) (``ID``, ``SM``, ``LB``, ``PU``, ``PL`` are all required and there are no params for ``KS``, ``PG``, or ``FO``). In terms of what is shown and what is required - this mirrors ``picard_AddOrReplaceReadGroups``.
|
|
854 - Just assign the ``ID`` and do so automatically (based either on collection or standalone dataset information). No extra form elements are shown to the user. (Should this be the new default?)
|
|
855 - Do not set read groups.
|
|
856 - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance).
|
|
857 - An example "mapper" test tool which demonstrates optionally including read groups.
|
|
858 - An example read group assign test tool which demonstrates unconditionally specifying macros.
|
|
859
|
|
860 In addition to unifying everything, the macro file defines enhanced ``ID``, ``SM``, and ``LB`` parameter inputs that are wrapped in a conditional. That conditional allows manual input but also allows the user to just say Galaxy should use collection information or dataset name (if input is not in a collection) to assign these parameters. This should simplify things and make simple workflows more robust, but is absolutely essential for collection-based workflows and newer tool form options that allow running a tool in parallel over many inputs.
|
|
861
|
|
862 This may look at first glance like it is really complicated - but if you focus just on the mappers for instance and treat the macro file like a library - the client interface is actually a good deal easier than doing this stuff by hand for each tool.
|
|
863
|
|
864 Updates from original version:
|
|
865
|
|
866 - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools.
|
|
867 - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments).
|
|
868 - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that).
|
|
869
|
|
870 Smaller Notes:
|
|
871
|
|
872 The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine:
|
|
873
|
|
874 ```
|
|
875 -@RG ID:rg1 SM: PL:CAPILLARY
|
|
876 -@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 SM: PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpn_I5mQ/files/000/dataset_9.dat /tmp/tmpn_I5mQ/files/000/dataset_10.dat
|
|
877 +@RG ID:rg1 PL:CAPILLARY
|
|
878 +@PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa sampe -r @RG ID:rg1 PL:CAPILLARY localref.fa first.sai second.sai /tmp/tmpmN3j1j/files/000/dataset_9.dat /tmp/tmpmN3j1j/files/000/dataset_10.dat
|
|
879 ```">Unify and collectionify read group handling.</a>
|
|
880 </span>
|
|
881 </td>
|
|
882 <td class="age">
|
|
883 <span class="css-truncate css-truncate-target"><time datetime="2015-05-07T19:31:09Z" is="time-ago">May 7, 2015</time></span>
|
|
884 </td>
|
|
885 </tr>
|
|
886 </tbody>
|
|
887 </table>
|
|
888
|
|
889 </div>
|
|
890
|
|
891
|
|
892
|
|
893
|
|
894
|
|
895 </div>
|
|
896 </div>
|
|
897 <div class="modal-backdrop"></div>
|
|
898 </div>
|
|
899 </div>
|
|
900
|
|
901
|
|
902 </div><!-- /.wrapper -->
|
|
903
|
|
904 <div class="container">
|
|
905 <div class="site-footer" role="contentinfo">
|
|
906 <ul class="site-footer-links right">
|
|
907 <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
|
|
908 <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
|
|
909 <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
|
|
910 <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li>
|
|
911 <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
|
|
912 <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li>
|
|
913 <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li>
|
|
914
|
|
915 </ul>
|
|
916
|
|
917 <a href="https://github.com" aria-label="Homepage">
|
|
918 <span class="mega-octicon octicon-mark-github" title="GitHub"></span>
|
|
919 </a>
|
|
920 <ul class="site-footer-links">
|
|
921 <li>© 2015 <span title="0.06882s from github-fe127-cp1-prd.iad.github.net">GitHub</span>, Inc.</li>
|
|
922 <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li>
|
|
923 <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li>
|
|
924 <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li>
|
|
925 <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li>
|
|
926 </ul>
|
|
927 </div>
|
|
928 </div>
|
|
929
|
|
930
|
|
931 <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay">
|
|
932 <div class="fullscreen-container js-suggester-container">
|
|
933 <div class="textarea-wrap">
|
|
934 <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder="" aria-label=""></textarea>
|
|
935 <div class="suggester-container">
|
|
936 <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div>
|
|
937 </div>
|
|
938 </div>
|
|
939 </div>
|
|
940 <div class="fullscreen-sidebar">
|
|
941 <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode">
|
|
942 <span class="mega-octicon octicon-screen-normal"></span>
|
|
943 </a>
|
|
944 <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w"
|
|
945 aria-label="Switch themes">
|
|
946 <span class="octicon octicon-color-mode"></span>
|
|
947 </a>
|
|
948 </div>
|
|
949 </div>
|
|
950
|
|
951
|
|
952
|
|
953
|
|
954
|
|
955
|
|
956 <div id="ajax-error-message" class="flash flash-error">
|
|
957 <span class="octicon octicon-alert"></span>
|
|
958 <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a>
|
|
959 Something went wrong with that request. Please try again.
|
|
960 </div>
|
|
961
|
|
962
|
|
963 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-eedcd4970c51d77d26b12825fc1fb1fbd554a880c0a8649a9cac6b63f1ee7cff.js"></script>
|
|
964 <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github/index-1af8eb3fd83c34afcee37eae4704e57d3bb35ccacee5574545665527ae02d731.js"></script>
|
|
965
|
|
966
|
|
967 </body>
|
|
968 </html>
|
|
969
|