Mercurial > repos > eduardo > download_and_align

comparison url2bowtie/tool-data/test-data2 @ 7:8accf8976cf7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author eduardo
date Mon, 03 Aug 2015 05:36:36 -0400
parents
children
comparison
equal deleted inserted replaced
6:18b04f0fb939 7:8accf8976cf7
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 · 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&amp;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&amp;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="&#x2713;" /></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 new…"
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&amp;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="&#x2713;" /><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="&#x2713;" /><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="&#x2713;" /><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="&#x2713;" /><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="&#x2713;" /><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&amp;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="&#x2713;" /><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&amp;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="&#x2713;" /><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&amp;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="&#x2713;" /><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 tag…" 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="&#x2713;" /><input name="authenticity_token" type="hidden" value="oHnhBUKtIFc/i+gj1F8SdSSK6r2vwLo0csLvt6huBR6W4GyuyAl915tvYyDR2eLrs8hxzyu3b0Ooq8FsVZjYww==" /></div>
653 <button class="btn-link tooltipped tooltipped-e" type="submit" data-disable-with="working…" 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 &quot;mapper&quot; 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&#39;t accept certain valid read groups arguments).
688 - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn&#39;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">…</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&amp;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 &quot;mapper&quot; 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&#39;t accept certain valid read groups arguments).
868 - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn&#39;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>&copy; 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