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289 <span class="js-select-button-text hidden-select-button-text">
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290 <span class="octicon octicon-mute"></span>
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291 Stop ignoring
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292 </span>
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293 </div>
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294 </div>
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295
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296 </div>
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297
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298 </div>
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299 </div>
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300 </div>
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301 </form>
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302 </li>
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303
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304 <li>
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305
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306 <div class="js-toggler-container js-social-container starring-container ">
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307
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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>
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309 <button
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310 class="btn btn-sm btn-with-count js-toggler-target"
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311 aria-label="Unstar this repository" title="Unstar galaxyproject/tools-devteam"
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312 data-ga-click="Repository, click unstar button, action:files#disambiguate; text:Unstar">
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313 <span class="octicon octicon-star"></span>
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314 Unstar
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315 </button>
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316 <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/stargazers">
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317 19
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318 </a>
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319 </form>
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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>
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321 <button
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322 class="btn btn-sm btn-with-count js-toggler-target"
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323 aria-label="Star this repository" title="Star galaxyproject/tools-devteam"
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324 data-ga-click="Repository, click star button, action:files#disambiguate; text:Star">
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325 <span class="octicon octicon-star"></span>
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326 Star
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327 </button>
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328 <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/stargazers">
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329 19
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330 </a>
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331 </form> </div>
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332
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333 </li>
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334
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335 <li>
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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>
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337 <button
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338 type="submit"
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339 class="btn btn-sm btn-with-count"
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340 data-ga-click="Repository, show fork modal, action:files#disambiguate; text:Fork"
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341 title="Fork your own copy of galaxyproject/tools-devteam to your account"
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342 aria-label="Fork your own copy of galaxyproject/tools-devteam to your account">
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343 <span class="octicon octicon-repo-forked"></span>
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344 Fork
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345 </button>
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346 <a href="/galaxyproject/tools-devteam/network" class="social-count">32</a>
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347 </form> </li>
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348
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349 </ul>
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350
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351 <h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public ">
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352 <span class="mega-octicon octicon-repo"></span>
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353 <span class="author"><a href="/galaxyproject" class="url fn" itemprop="url" rel="author"><span itemprop="title">galaxyproject</span></a></span><!--
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354 --><span class="path-divider">/</span><!--
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355 --><strong><a href="/galaxyproject/tools-devteam" data-pjax="#js-repo-pjax-container">tools-devteam</a></strong>
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356
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357 <span class="page-context-loader">
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358 <img alt="" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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359 </span>
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360
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361 </h1>
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362 </div>
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363
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364 </div>
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365 </div>
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366
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367 <div class="container">
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368 <div class="repository-with-sidebar repo-container new-discussion-timeline ">
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369 <div class="repository-sidebar clearfix">
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370
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371
|
|
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372 <nav class="sunken-menu repo-nav js-repo-nav js-sidenav-container-pjax js-octicon-loaders"
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373 role="navigation"
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374 data-pjax="#js-repo-pjax-container"
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375 data-issue-count-url="/galaxyproject/tools-devteam/issues/counts">
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376 <ul class="sunken-menu-group">
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377 <li class="tooltipped tooltipped-w" aria-label="Code">
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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">
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379 <span class="octicon octicon-code"></span> <span class="full-word">Code</span>
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380 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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381 </a> </li>
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382
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383 <li class="tooltipped tooltipped-w" aria-label="Issues">
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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">
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385 <span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span>
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386 <span class="js-issue-replace-counter"></span>
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387 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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388 </a> </li>
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389
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390 <li class="tooltipped tooltipped-w" aria-label="Pull requests">
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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">
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392 <span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull requests</span>
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393 <span class="js-pull-replace-counter"></span>
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394 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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395 </a> </li>
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396
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397 <li class="tooltipped tooltipped-w" aria-label="Wiki">
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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">
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399 <span class="octicon octicon-book"></span> <span class="full-word">Wiki</span>
|
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400 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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401 </a> </li>
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402 </ul>
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403 <div class="sunken-menu-separator"></div>
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404 <ul class="sunken-menu-group">
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405
|
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406 <li class="tooltipped tooltipped-w" aria-label="Pulse">
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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">
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408 <span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span>
|
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|
409 <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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410 </a> </li>
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411
|
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412 <li class="tooltipped tooltipped-w" aria-label="Graphs">
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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">
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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" />
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416 </a> </li>
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417 </ul>
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418
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419
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420 </nav>
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421
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422 <div class="only-with-full-nav">
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423
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424 <div class="js-clone-url clone-url open"
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425 data-protocol-type="http">
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426 <h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
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427 <div class="input-group js-zeroclipboard-container">
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428 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
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429 value="https://github.com/galaxyproject/tools-devteam.git" readonly="readonly" aria-label="HTTPS clone URL">
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430 <span class="input-group-button">
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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>
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432 </span>
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433 </div>
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434 </div>
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435
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436
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437 <div class="js-clone-url clone-url "
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438 data-protocol-type="ssh">
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439 <h3><span class="text-emphasized">SSH</span> clone URL</h3>
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440 <div class="input-group js-zeroclipboard-container">
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441 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
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442 value="git@github.com:galaxyproject/tools-devteam.git" readonly="readonly" aria-label="SSH clone URL">
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443 <span class="input-group-button">
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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>
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445 </span>
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446 </div>
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447 </div>
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448
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449
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450 <div class="js-clone-url clone-url "
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451 data-protocol-type="subversion">
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452 <h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
|
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453 <div class="input-group js-zeroclipboard-container">
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454 <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
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455 value="https://github.com/galaxyproject/tools-devteam" readonly="readonly" aria-label="Subversion checkout URL">
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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>
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458 </span>
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459 </div>
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460 </div>
|
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461
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462
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463
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464 <div class="clone-options">You can clone with
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|
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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>.
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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.">
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467 <span class="octicon octicon-question"></span>
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468 </a>
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469 </div>
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470
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471 <a href="/galaxyproject/tools-devteam/archive/master.zip"
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472 class="btn btn-sm sidebar-button"
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473 aria-label="Download the contents of galaxyproject/tools-devteam as a zip file"
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474 title="Download the contents of galaxyproject/tools-devteam as a zip file"
|
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|
475 rel="nofollow">
|
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476 <span class="octicon octicon-cloud-download"></span>
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477 Download ZIP
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478 </a>
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479 </div>
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480 </div>
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481 <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container>
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482
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483
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484 <div class="file-navigation">
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485
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486 <div class="select-menu js-menu-container js-select-menu left">
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487 <span class="btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w"
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488 data-ref="master"
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489 title="master"
|
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|
490 role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true">
|
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491 <i>Branch:</i>
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492 <span class="js-select-button css-truncate-target">master</span>
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493 </span>
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494
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495 <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true">
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496
|
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497 <div class="select-menu-modal">
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498 <div class="select-menu-header">
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499 <span class="select-menu-title">Switch branches/tags</span>
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500 <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
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501 </div>
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502
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503 <div class="select-menu-filters">
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504 <div class="select-menu-text-filter">
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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">
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506 </div>
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507 <div class="select-menu-tabs">
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508 <ul>
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509 <li class="select-menu-tab">
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510 <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a>
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511 </li>
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512 <li class="select-menu-tab">
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513 <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tagโฆ" class="js-select-menu-tab" role="tab">Tags</a>
|
|
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514 </li>
|
|
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515 </ul>
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516 </div>
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517 </div>
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518
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519 <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu">
|
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520
|
|
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521 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
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522
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523
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524 <a class="select-menu-item js-navigation-item js-navigation-open "
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|
525 href="/galaxyproject/tools-devteam/tree/bamtools/tools/bowtie2/test-data"
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526 data-name="bamtools"
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527 data-skip-pjax="true"
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528 rel="nofollow">
|
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|
529 <span class="select-menu-item-icon octicon octicon-check"></span>
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530 <span class="select-menu-item-text css-truncate-target" title="bamtools">
|
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|
531 bamtools
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532 </span>
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533 </a>
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534 <a class="select-menu-item js-navigation-item js-navigation-open "
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535 href="/galaxyproject/tools-devteam/tree/bamtools_images/tools/bowtie2/test-data"
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|
536 data-name="bamtools_images"
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|
537 data-skip-pjax="true"
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538 rel="nofollow">
|
|
|
539 <span class="select-menu-item-icon octicon octicon-check"></span>
|
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540 <span class="select-menu-item-text css-truncate-target" title="bamtools_images">
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541 bamtools_images
|
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542 </span>
|
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543 </a>
|
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544 <a class="select-menu-item js-navigation-item js-navigation-open "
|
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545 href="/galaxyproject/tools-devteam/tree/blankenberg-dm-samtools-fix-1/tools/bowtie2/test-data"
|
|
|
546 data-name="blankenberg-dm-samtools-fix-1"
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547 data-skip-pjax="true"
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548 rel="nofollow">
|
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|
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">
|
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551 blankenberg-dm-samtools-fix-1
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552 </span>
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553 </a>
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554 <a class="select-menu-item js-navigation-item js-navigation-open "
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603 </a>
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610 <span class="select-menu-item-text css-truncate-target" title="picard_sortsam">
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611 picard_sortsam
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612 </span>
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613 </a>
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614 <a class="select-menu-item js-navigation-item js-navigation-open "
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647 <span class="octicon octicon-history"></span>
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648 </a>
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650 <div class="breadcrumb">
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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>
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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>
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653 <button class="btn-link tooltipped tooltipped-e" type="submit" data-disable-with="workingโฆ" aria-label="Fork this project and create a new file">
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662
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663 <div class="commit commit-tease js-details-container" >
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664 <p class="commit-title ">
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665 <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling.
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666
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667 The reusable macro file has:
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668
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669 - Defines widgets for common read group parameters.
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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).
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671 - The conditional (used by mappers) has fours modes:
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672 - Set according the specification (only ID required - has all parameters). Current BWA approach.
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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``.
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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?)
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675 - Do not set read groups.
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676 - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance).
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677 - An example "mapper" test tool which demonstrates optionally including read groups.
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678 - An example read group assign test tool which demonstrates unconditionally specifying macros.
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679
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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.
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681
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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.
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683
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684 Updates from original version:
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685
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686 - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools.
|
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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).
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688 - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that).
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689
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690 Smaller Notes:
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691
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692 The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine:
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693
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694 ```
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695 -@RG ID:rg1 SM: PL:CAPILLARY
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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
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697 +@RG ID:rg1 PL:CAPILLARY
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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
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699 ```">Unify and collectionify read group handling.</a>
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700 <span class="hidden-text-expander inline"><a href="#" class="js-details-target">โฆ</a></span>
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701 </p>
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702 <div class="commit-desc"><pre>The reusable macro file has:
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703
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704 - Defines widgets for common read group parameters.
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|
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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:
|
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728
|
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729 ```
|
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|
730 -<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 SM: PL:CAPILLARY
|
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|
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
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732 +<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 PL:CAPILLARY
|
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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
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734 ```</pre></div>
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735 <div class="commit-meta">
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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>
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737 <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="sha-block" data-pjax>latest commit <span class="sha">d0e3412c58</span></a>
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738
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739 <div class="authorship">
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740 <img alt="@jmchilton" class="avatar" height="20" src="https://avatars0.githubusercontent.com/u/216771?v=3&s=40" width="20" />
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741 <span class="author-name"><a href="/jmchilton" rel="contributor">jmchilton</a></span>
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742 authored <time class="updated" datetime="2015-04-13T20:08:40Z" is="relative-time">Apr 13, 2015</time>
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743
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744 </div>
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745 </div>
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746 </div>
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747
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748
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749 <div class="file-wrap">
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750 <a href="/galaxyproject/tools-devteam/tree/22227a626113448672603f832bdccba36dd3fdac/tools/bowtie2/test-data" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a>
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751
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752 <table class="files" data-pjax>
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753 <tr class="up-tree">
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754 <td></td>
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755 <td><a href="/galaxyproject/tools-devteam/tree/master/tools/bowtie2" rel="nofollow" title="Go to parent directory">..</a></td>
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756 <td></td>
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761 <tbody>
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762 <tr class="warning include-fragment-error">
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764 <td class="content" colspan="3">Failed to load latest commit information.</td>
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765 </tr>
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766
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770 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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771 </td>
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772 <td class="content">
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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>
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774 </td>
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775 <td class="message">
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776 <span class="css-truncate css-truncate-target">
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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>
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778 </span>
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779 </td>
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780 <td class="age">
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781 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
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782 </td>
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783 </tr>
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784 <tr>
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787 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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788 </td>
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789 <td class="content">
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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>
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791 </td>
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792 <td class="message">
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793 <span class="css-truncate css-truncate-target">
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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>
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795 </span>
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796 </td>
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797 <td class="age">
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798 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
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799 </td>
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800 </tr>
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801 <tr>
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802 <td class="icon">
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803 <span class="octicon octicon-file-text"></span>
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804 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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805 </td>
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806 <td class="content">
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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>
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808 </td>
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809 <td class="message">
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810 <span class="css-truncate css-truncate-target">
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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>
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812 </span>
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813 </td>
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814 <td class="age">
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815 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
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816 </td>
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817 </tr>
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818 <tr>
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819 <td class="icon">
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820 <span class="octicon octicon-file-text"></span>
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821 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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822 </td>
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823 <td class="content">
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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>
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825 </td>
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826 <td class="message">
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827 <span class="css-truncate css-truncate-target">
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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>
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829 </span>
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830 </td>
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831 <td class="age">
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832 <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span>
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833 </td>
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834 </tr>
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835 <tr>
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836 <td class="icon">
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837 <span class="octicon octicon-file-text"></span>
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838 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
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839 </td>
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840 <td class="content">
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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>
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842 </td>
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843 <td class="message">
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844 <span class="css-truncate css-truncate-target">
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845 <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling.
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846
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847 The reusable macro file has:
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848
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849 - Defines widgets for common read group parameters.
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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).
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851 - The conditional (used by mappers) has fours modes:
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852 - Set according the specification (only ID required - has all parameters). Current BWA approach.
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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``.
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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?)
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855 - Do not set read groups.
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856 - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance).
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857 - An example "mapper" test tool which demonstrates optionally including read groups.
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858 - An example read group assign test tool which demonstrates unconditionally specifying macros.
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859
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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.
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861
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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.
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863
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864 Updates from original version:
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865
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866 - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools.
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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).
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868 - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that).
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869
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870 Smaller Notes:
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871
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872 The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine:
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873
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874 ```
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875 -@RG ID:rg1 SM: PL:CAPILLARY
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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
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877 +@RG ID:rg1 PL:CAPILLARY
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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
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879 ```">Unify and collectionify read group handling.</a>
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880 </span>
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881 </td>
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882 <td class="age">
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883 <span class="css-truncate css-truncate-target"><time datetime="2015-05-07T19:31:09Z" is="time-ago">May 7, 2015</time></span>
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884 </td>
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885 </tr>
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886 </tbody>
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887 </table>
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888
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889 </div>
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