Mercurial > repos > eduardo > download_and_align
changeset 10:8a98bfab4d56
Cleanup
| author | Eduardo <eduardoalves@abdn.ac.uk> |
|---|---|
| date | Mon, 03 Aug 2015 11:19:46 +0100 |
| parents | 48006f05c208 |
| children | 9b8f92d9fcac |
| files | tool-data/bowtie2_indices.loc.sample url2bowtie/tool-data/bowtie2_indices.loc.sample url2bowtie/tool-data/test-data2 |
| diffstat | 3 files changed, 37 insertions(+), 1006 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie2_indices.loc.sample Mon Aug 03 11:19:46 2015 +0100 @@ -0,0 +1,37 @@ +# bowtie2_indices.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# So, for example, if you had hg18 indexes stored in: +# +# /depot/data2/galaxy/hg19/bowtie2/ +# +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 +# +# then the bowtie2_indices.loc entry could look like this: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 +# +#
--- a/url2bowtie/tool-data/bowtie2_indices.loc.sample Mon Aug 03 05:44:04 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -# bowtie2_indices.loc.sample -# This is a *.loc.sample file distributed with Galaxy that enables tools -# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. -# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup -# First create these data files and save them in your own data directory structure. -# Then, create a bowtie_indices.loc file to use those indexes with tools. -# Copy this file, save it with the same name (minus the .sample), -# follow the format examples, and store the result in this directory. -# The file should include an one line entry for each index set. -# The path points to the "basename" for the set, not a specific file. -# It has four text columns seperated by TABS. -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> -# -# So, for example, if you had hg18 indexes stored in: -# -# /depot/data2/galaxy/hg19/bowtie2/ -# -# containing hg19 genome and hg19.*.bt2 files, such as: -# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa -# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 -# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 -# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 -# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 -# -# then the bowtie2_indices.loc entry could look like this: -# -#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon -# -#More examples: -# -#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 -#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 -# -#
--- a/url2bowtie/tool-data/test-data2 Mon Aug 03 05:44:04 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,969 +0,0 @@ - - - -<!DOCTYPE html> -<html lang="en" class=""> - <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#"> - <meta charset='utf-8'> - <meta http-equiv="X-UA-Compatible" content="IE=edge"> - <meta http-equiv="Content-Language" content="en"> - <meta name="viewport" content="width=1020"> - - - <title>tools-devteam/tools/bowtie2/test-data at master · galaxyproject/tools-devteam</title> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> - <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png"> - <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144.png"> - <meta property="fb:app_id" content="1401488693436528"> - - <meta content="@github" name="twitter:site" /><meta content="summary" name="twitter:card" /><meta content="galaxyproject/tools-devteam" name="twitter:title" /><meta content="tools-devteam - Contains a set of Galaxy Tools mostly written by the Galaxy Team." name="twitter:description" /><meta content="https://avatars2.githubusercontent.com/u/7937847?v=3&s=400" name="twitter:image:src" /> - <meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars2.githubusercontent.com/u/7937847?v=3&s=400" property="og:image" /><meta content="galaxyproject/tools-devteam" property="og:title" /><meta content="https://github.com/galaxyproject/tools-devteam" property="og:url" /><meta content="tools-devteam - Contains a set of Galaxy Tools mostly written by the Galaxy Team." property="og:description" /> - <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> - <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors"> - <link rel="assets" href="https://assets-cdn.github.com/"> - <link rel="web-socket" href="wss://live.github.com/_sockets/OTc3Njk3Nzo0M2VmMGIwODU0ZjU3ZWUxZThhZWIwMzY1MjMxOTE1ODo4ZTQ0Y2E0ODgwZDM3MTJiNWRhNWVlOTUyOGM5ODNlNTZhZjQxMDQ5MDYwYzU0ZGY5NTY5Mzc1YTJkOTNkNjYw--f73b909c7c1527a9b16c59ffb4ec09a14213234b"> - <meta name="pjax-timeout" content="1000"> - <link rel="sudo-modal" href="/sessions/sudo_modal"> - - <meta name="msapplication-TileImage" content="/windows-tile.png"> - <meta name="msapplication-TileColor" content="#ffffff"> - <meta name="selected-link" value="repo_source" data-pjax-transient> - - <meta name="google-analytics" content="UA-3769691-2"> - - <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" /> - - <meta content="Rails, view, files#disambiguate" data-pjax-transient="true" name="analytics-event" /> - <meta class="js-ga-set" name="dimension1" content="Logged In"> - <meta class="js-ga-set" name="dimension4" content="Current repo nav"> - <meta name="is-dotcom" content="true"> - <meta name="hostname" content="github.com"> - <meta name="user-login" content="Eduardo-Alves"> - - <link rel="icon" sizes="any" mask href="https://assets-cdn.github.com/pinned-octocat.svg"> - <meta name="theme-color" content="#4078c0"> - <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico"> - - <!-- </textarea> --><!-- '"` --><meta content="authenticity_token" name="csrf-param" /> -<meta content="sIPcOPJvZdTd08u39MkUQ/PUyKwsCvX894Dnj44snbI93uW0BUf/KxzFCKGGP95A7rkJXNTeIYkid/7aVVwPVA==" name="csrf-token" /> - - - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github/index-c7126cd67871e693a9f863b7a0e99879ca39079b15a8784f8b543c03bf14ad72.css" media="all" rel="stylesheet" /> - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github2/index-87247f16e6450ef54cb0eda3f8f1484e33a3f18c7a7d3df1f76f67cba36a8d6d.css" media="all" rel="stylesheet" /> - - - - - <meta http-equiv="x-pjax-version" content="f8fdf7d6713452aadb5c847c2e94f51b"> - - - <meta name="description" content="tools-devteam - Contains a set of Galaxy Tools mostly written by the Galaxy Team."> - <meta name="go-import" content="github.com/galaxyproject/tools-devteam git https://github.com/galaxyproject/tools-devteam.git"> - - <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" /> - <link href="https://github.com/galaxyproject/tools-devteam/commits/master.atom" rel="alternate" title="Recent Commits to tools-devteam:master" type="application/atom+xml"> - - </head> - - - <body class="logged_in env-production linux vis-public"> - <a href="#start-of-content" tabindex="1" class="accessibility-aid js-skip-to-content">Skip to content</a> - <div class="wrapper"> - - - - - - - <div class="header header-logged-in true" role="banner"> - <div class="container clearfix"> - - <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"> - <span class="mega-octicon octicon-mark-github"></span> -</a> - - - <div class="site-search repo-scope js-site-search" role="search"> - <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/galaxyproject/tools-devteam/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/galaxyproject/tools-devteam/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> - <label class="js-chromeless-input-container form-control"> - <div class="scope-badge">This repository</div> - <input type="text" - class="js-site-search-focus js-site-search-field is-clearable chromeless-input" - data-hotkey="s" - name="q" - placeholder="Search" - aria-label="Search this repository" - data-global-scope-placeholder="Search GitHub" - data-repo-scope-placeholder="Search" - tabindex="1" - autocapitalize="off"> - </label> -</form> - </div> - - <ul class="header-nav left" role="navigation"> - <li class="header-nav-item"> - <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"> - Pull requests -</a> </li> - <li class="header-nav-item"> - <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"> - Issues -</a> </li> - <li class="header-nav-item"> - <a class="header-nav-link" href="https://gist.github.com/" data-ga-click="Header, go to gist, text:gist">Gist</a> - </li> - </ul> - - -<ul class="header-nav user-nav right" id="user-links"> - <li class="header-nav-item"> - <span class="js-socket-channel js-updatable-content" - data-channel="notification-changed:Eduardo-Alves" - data-url="/notifications/header"> - <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"> - <span class="mail-status all-read"></span> - <span class="octicon octicon-inbox"></span> -</a> </span> - - </li> - - <li class="header-nav-item dropdown js-menu-container"> - <a class="header-nav-link tooltipped tooltipped-s js-menu-target" href="/new" - aria-label="Create new…" - data-ga-click="Header, create new, icon:add"> - <span class="octicon octicon-plus left"></span> - <span class="dropdown-caret"></span> - </a> - - <div class="dropdown-menu-content js-menu-content"> - <ul class="dropdown-menu dropdown-menu-sw"> - -<a class="dropdown-item" href="/new" data-ga-click="Header, create new repository"> - New repository -</a> - - - <a class="dropdown-item" href="/organizations/new" data-ga-click="Header, create new organization"> - New organization - </a> - - - - <div class="dropdown-divider"></div> - <div class="dropdown-header"> - <span title="galaxyproject/tools-devteam">This repository</span> - </div> - <a class="dropdown-item" href="/galaxyproject/tools-devteam/issues/new" data-ga-click="Header, create new issue"> - New issue - </a> - - </ul> - </div> - </li> - - <li class="header-nav-item dropdown js-menu-container"> - <a class="header-nav-link name tooltipped tooltipped-s js-menu-target" href="/Eduardo-Alves" - aria-label="View profile and more" - data-ga-click="Header, show menu, icon:avatar"> - <img alt="@Eduardo-Alves" class="avatar" height="20" src="https://avatars1.githubusercontent.com/u/9776977?v=3&s=40" width="20" /> - <span class="dropdown-caret"></span> - </a> - - <div class="dropdown-menu-content js-menu-content"> - <div class="dropdown-menu dropdown-menu-sw"> - <div class="dropdown-header header-nav-current-user css-truncate"> - Signed in as <strong class="css-truncate-target">Eduardo-Alves</strong> - </div> - <div class="dropdown-divider"></div> - - <a class="dropdown-item" href="/Eduardo-Alves" data-ga-click="Header, go to profile, text:your profile"> - Your profile - </a> - <a class="dropdown-item" href="/stars" data-ga-click="Header, go to starred repos, text:your stars"> - Your stars - </a> - <a class="dropdown-item" href="/explore" data-ga-click="Header, go to explore, text:explore"> - Explore - </a> - <a class="dropdown-item" href="https://help.github.com" data-ga-click="Header, go to help, text:help"> - Help - </a> - <div class="dropdown-divider"></div> - - <a class="dropdown-item" href="/settings/profile" data-ga-click="Header, go to settings, icon:settings"> - Settings - </a> - - <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/logout" class="logout-form" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="fMiuMnZEhOyhrkDmQMsMGi4+rgqhqa/5AyAG+2bEQj/sNUfzQZ3FUFyIjO15HQuxl0IIXgOxpQ+/rGZ4GamDuA==" /></div> - <button class="dropdown-item dropdown-signout" data-ga-click="Header, sign out, icon:logout"> - Sign out - </button> -</form> </div> - </div> - </li> -</ul> - - - - </div> -</div> - - - - - - - <div id="start-of-content" class="accessibility-aid"></div> - <div class="site" itemscope itemtype="http://schema.org/WebPage"> - <div id="js-flash-container"> - - </div> - <div class="pagehead repohead instapaper_ignore readability-menu "> - <div class="container"> - - <div class="clearfix"> - -<ul class="pagehead-actions"> - - <li> - <!-- </textarea> --><!-- '"` --><form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" data-form-nonce="1a2e7c5c235fe6fddd1652a8fbf52781a0304796" data-remote="true" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="DGdw+xCuQFxtIYNwCNm6pBV1JG27b3WKuUifr1dYxp0y2kRvMyTGOVGs0z/mJP2iVSvhaoCMK/7UQID8gHh2Bg==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="24609401" /> - - <div class="select-menu js-menu-container js-select-menu"> - <a href="/galaxyproject/tools-devteam/subscription" - class="btn btn-sm btn-with-count select-menu-button js-menu-target" role="button" tabindex="0" aria-haspopup="true" - data-ga-click="Repository, click Watch settings, action:files#disambiguate"> - <span class="js-select-button"> - <span class="octicon octicon-eye"></span> - Watch - </span> - </a> - <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/watchers"> - 24 - </a> - - <div class="select-menu-modal-holder"> - <div class="select-menu-modal subscription-menu-modal js-menu-content" aria-hidden="true"> - <div class="select-menu-header"> - <span class="select-menu-title">Notifications</span> - <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span> - </div> - - <div class="select-menu-list js-navigation-container" role="menu"> - - <div class="select-menu-item js-navigation-item selected" role="menuitem" tabindex="0"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <div class="select-menu-item-text"> - <input checked="checked" id="do_included" name="do" type="radio" value="included" /> - <span class="select-menu-item-heading">Not watching</span> - <span class="description">Be notified when participating or @mentioned.</span> - <span class="js-select-button-text hidden-select-button-text"> - <span class="octicon octicon-eye"></span> - Watch - </span> - </div> - </div> - - <div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0"> - <span class="select-menu-item-icon octicon octicon octicon-check"></span> - <div class="select-menu-item-text"> - <input id="do_subscribed" name="do" type="radio" value="subscribed" /> - <span class="select-menu-item-heading">Watching</span> - <span class="description">Be notified of all conversations.</span> - <span class="js-select-button-text hidden-select-button-text"> - <span class="octicon octicon-eye"></span> - Unwatch - </span> - </div> - </div> - - <div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <div class="select-menu-item-text"> - <input id="do_ignore" name="do" type="radio" value="ignore" /> - <span class="select-menu-item-heading">Ignoring</span> - <span class="description">Never be notified.</span> - <span class="js-select-button-text hidden-select-button-text"> - <span class="octicon octicon-mute"></span> - Stop ignoring - </span> - </div> - </div> - - </div> - - </div> - </div> - </div> -</form> - </li> - - <li> - - <div class="js-toggler-container js-social-container starring-container "> - - <!-- </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> - <button - class="btn btn-sm btn-with-count js-toggler-target" - aria-label="Unstar this repository" title="Unstar galaxyproject/tools-devteam" - data-ga-click="Repository, click unstar button, action:files#disambiguate; text:Unstar"> - <span class="octicon octicon-star"></span> - Unstar - </button> - <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/stargazers"> - 19 - </a> -</form> - <!-- </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> - <button - class="btn btn-sm btn-with-count js-toggler-target" - aria-label="Star this repository" title="Star galaxyproject/tools-devteam" - data-ga-click="Repository, click star button, action:files#disambiguate; text:Star"> - <span class="octicon octicon-star"></span> - Star - </button> - <a class="social-count js-social-count" href="/galaxyproject/tools-devteam/stargazers"> - 19 - </a> -</form> </div> - - </li> - - <li> - <!-- </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> - <button - type="submit" - class="btn btn-sm btn-with-count" - data-ga-click="Repository, show fork modal, action:files#disambiguate; text:Fork" - title="Fork your own copy of galaxyproject/tools-devteam to your account" - aria-label="Fork your own copy of galaxyproject/tools-devteam to your account"> - <span class="octicon octicon-repo-forked"></span> - Fork - </button> - <a href="/galaxyproject/tools-devteam/network" class="social-count">32</a> -</form> </li> - -</ul> - - <h1 itemscope itemtype="http://data-vocabulary.org/Breadcrumb" class="entry-title public "> - <span class="mega-octicon octicon-repo"></span> - <span class="author"><a href="/galaxyproject" class="url fn" itemprop="url" rel="author"><span itemprop="title">galaxyproject</span></a></span><!-- - --><span class="path-divider">/</span><!-- - --><strong><a href="/galaxyproject/tools-devteam" data-pjax="#js-repo-pjax-container">tools-devteam</a></strong> - - <span class="page-context-loader"> - <img alt="" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </span> - - </h1> - </div> - - </div> - </div> - - <div class="container"> - <div class="repository-with-sidebar repo-container new-discussion-timeline "> - <div class="repository-sidebar clearfix"> - - -<nav class="sunken-menu repo-nav js-repo-nav js-sidenav-container-pjax js-octicon-loaders" - role="navigation" - data-pjax="#js-repo-pjax-container" - data-issue-count-url="/galaxyproject/tools-devteam/issues/counts"> - <ul class="sunken-menu-group"> - <li class="tooltipped tooltipped-w" aria-label="Code"> - <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"> - <span class="octicon octicon-code"></span> <span class="full-word">Code</span> - <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> -</a> </li> - - <li class="tooltipped tooltipped-w" aria-label="Issues"> - <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"> - <span class="octicon octicon-issue-opened"></span> <span class="full-word">Issues</span> - <span class="js-issue-replace-counter"></span> - <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> -</a> </li> - - <li class="tooltipped tooltipped-w" aria-label="Pull requests"> - <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"> - <span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull requests</span> - <span class="js-pull-replace-counter"></span> - <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> -</a> </li> - - <li class="tooltipped tooltipped-w" aria-label="Wiki"> - <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"> - <span class="octicon octicon-book"></span> <span class="full-word">Wiki</span> - <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> -</a> </li> - </ul> - <div class="sunken-menu-separator"></div> - <ul class="sunken-menu-group"> - - <li class="tooltipped tooltipped-w" aria-label="Pulse"> - <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"> - <span class="octicon octicon-pulse"></span> <span class="full-word">Pulse</span> - <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> -</a> </li> - - <li class="tooltipped tooltipped-w" aria-label="Graphs"> - <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"> - <span class="octicon octicon-graph"></span> <span class="full-word">Graphs</span> - <img alt="" class="mini-loader" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> -</a> </li> - </ul> - - -</nav> - - <div class="only-with-full-nav"> - -<div class="js-clone-url clone-url open" - data-protocol-type="http"> - <h3><span class="text-emphasized">HTTPS</span> clone URL</h3> - <div class="input-group js-zeroclipboard-container"> - <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target" - value="https://github.com/galaxyproject/tools-devteam.git" readonly="readonly" aria-label="HTTPS clone URL"> - <span class="input-group-button"> - <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> - </span> - </div> -</div> - - -<div class="js-clone-url clone-url " - data-protocol-type="ssh"> - <h3><span class="text-emphasized">SSH</span> clone URL</h3> - <div class="input-group js-zeroclipboard-container"> - <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target" - value="git@github.com:galaxyproject/tools-devteam.git" readonly="readonly" aria-label="SSH clone URL"> - <span class="input-group-button"> - <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> - </span> - </div> -</div> - - -<div class="js-clone-url clone-url " - data-protocol-type="subversion"> - <h3><span class="text-emphasized">Subversion</span> checkout URL</h3> - <div class="input-group js-zeroclipboard-container"> - <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target" - value="https://github.com/galaxyproject/tools-devteam" readonly="readonly" aria-label="Subversion checkout URL"> - <span class="input-group-button"> - <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> - </span> - </div> -</div> - - - - <div class="clone-options">You can clone with - <!-- </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>. - <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."> - <span class="octicon octicon-question"></span> - </a> - </div> - - <a href="/galaxyproject/tools-devteam/archive/master.zip" - class="btn btn-sm sidebar-button" - aria-label="Download the contents of galaxyproject/tools-devteam as a zip file" - title="Download the contents of galaxyproject/tools-devteam as a zip file" - rel="nofollow"> - <span class="octicon octicon-cloud-download"></span> - Download ZIP - </a> - </div> - </div> - <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container> - - - <div class="file-navigation"> - -<div class="select-menu js-menu-container js-select-menu left"> - <span class="btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w" - data-ref="master" - title="master" - role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true"> - <i>Branch:</i> - <span class="js-select-button css-truncate-target">master</span> - </span> - - <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true"> - - <div class="select-menu-modal"> - <div class="select-menu-header"> - <span class="select-menu-title">Switch branches/tags</span> - <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span> - </div> - - <div class="select-menu-filters"> - <div class="select-menu-text-filter"> - <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags"> - </div> - <div class="select-menu-tabs"> - <ul> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a> - </li> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab" role="tab">Tags</a> - </li> - </ul> - </div> - </div> - - <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu"> - - <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> - - - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/bamtools/tools/bowtie2/test-data" - data-name="bamtools" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="bamtools"> - bamtools - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/bamtools_images/tools/bowtie2/test-data" - data-name="bamtools_images" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="bamtools_images"> - bamtools_images - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/blankenberg-dm-samtools-fix-1/tools/bowtie2/test-data" - data-name="blankenberg-dm-samtools-fix-1" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="blankenberg-dm-samtools-fix-1"> - blankenberg-dm-samtools-fix-1 - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/hisat/tools/bowtie2/test-data" - data-name="hisat" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="hisat"> - hisat - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/libgd-export/tools/bowtie2/test-data" - data-name="libgd-export" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="libgd-export"> - libgd-export - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open selected" - href="/galaxyproject/tools-devteam/tree/master/tools/bowtie2/test-data" - data-name="master" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="master"> - master - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/origin/hisat/tools/bowtie2/test-data" - data-name="origin/hisat" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="origin/hisat"> - origin/hisat - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/osx_compat/tools/bowtie2/test-data" - data-name="osx_compat" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="osx_compat"> - osx_compat - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/picard_sortsam/tools/bowtie2/test-data" - data-name="picard_sortsam" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="picard_sortsam"> - picard_sortsam - </span> - </a> - <a class="select-menu-item js-navigation-item js-navigation-open " - href="/galaxyproject/tools-devteam/tree/weblogo-fix/tools/bowtie2/test-data" - data-name="weblogo-fix" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="weblogo-fix"> - weblogo-fix - </span> - </a> - </div> - - <div class="select-menu-no-results">Nothing to show</div> - </div> - - <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags"> - <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> - - - </div> - - <div class="select-menu-no-results">Nothing to show</div> - </div> - - </div> - </div> -</div> - - <div class="btn-group right"> - <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"> - <span class="octicon octicon-list-unordered"></span> - </a> - <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"> - <span class="octicon octicon-history"></span> - </a> - </div> - <div class="breadcrumb"> - <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> - <!-- </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> - <button class="btn-link tooltipped tooltipped-e" type="submit" data-disable-with="working…" aria-label="Fork this project and create a new file"> - <span class="js-new-blob-submit octicon octicon-plus"></span> - </button> -</form> - </div> - </div> - - - - - <div class="commit commit-tease js-details-container" > - <p class="commit-title "> - <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling. - -The reusable macro file has: - - - Defines widgets for common read group parameters. - - 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). - - The conditional (used by mappers) has fours modes: - - Set according the specification (only ID required - has all parameters). Current BWA approach. - - 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``. - - 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?) - - Do not set read groups. - - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance). - - An example "mapper" test tool which demonstrates optionally including read groups. - - An example read group assign test tool which demonstrates unconditionally specifying macros. - -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. - -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. - -Updates from original version: - - - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools. - - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments). - - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that). - -Smaller Notes: - -The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine: - -``` --@RG ID:rg1 SM: PL:CAPILLARY --@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 -+@RG ID:rg1 PL:CAPILLARY -+@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 -```">Unify and collectionify read group handling.</a> - <span class="hidden-text-expander inline"><a href="#" class="js-details-target">…</a></span> - </p> - <div class="commit-desc"><pre>The reusable macro file has: - - - Defines widgets for common read group parameters. - - 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). - - The conditional (used by mappers) has fours modes: - - Set according the specification (only ID required - has all parameters). Current BWA approach. - - 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``. - - 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?) - - Do not set read groups. - - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance). - - An example "mapper" test tool which demonstrates optionally including read groups. - - An example read group assign test tool which demonstrates unconditionally specifying macros. - -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. - -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. - -Updates from original version: - - - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools. - - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments). - - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that). - -Smaller Notes: - -The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine: - -``` --<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 SM: PL:CAPILLARY --<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 -+<a href="https://github.com/RG" class="user-mention">@RG</a> ID:rg1 PL:CAPILLARY -+<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 -```</pre></div> - <div class="commit-meta"> - <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> - <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="sha-block" data-pjax>latest commit <span class="sha">d0e3412c58</span></a> - - <div class="authorship"> - <img alt="@jmchilton" class="avatar" height="20" src="https://avatars0.githubusercontent.com/u/216771?v=3&s=40" width="20" /> - <span class="author-name"><a href="/jmchilton" rel="contributor">jmchilton</a></span> - authored <time class="updated" datetime="2015-04-13T20:08:40Z" is="relative-time">Apr 13, 2015</time> - - </div> - </div> - </div> - - -<div class="file-wrap"> - <a href="/galaxyproject/tools-devteam/tree/22227a626113448672603f832bdccba36dd3fdac/tools/bowtie2/test-data" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a> - - <table class="files" data-pjax> - <tr class="up-tree"> - <td></td> - <td><a href="/galaxyproject/tools-devteam/tree/master/tools/bowtie2" rel="nofollow" title="Go to parent directory">..</a></td> - <td></td> - <td></td> - </tr> - - - <tbody> - <tr class="warning include-fragment-error"> - <td class="icon"><span class="octicon octicon-alert"></span></td> - <td class="content" colspan="3">Failed to load latest commit information.</td> - </tr> - - <tr> - <td class="icon"> - <span class="octicon octicon-file-text"></span> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <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> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span> - </td> - </tr> - <tr> - <td class="icon"> - <span class="octicon octicon-file-text"></span> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <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> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span> - </td> - </tr> - <tr> - <td class="icon"> - <span class="octicon octicon-file-text"></span> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <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> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span> - </td> - </tr> - <tr> - <td class="icon"> - <span class="octicon octicon-file-text"></span> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <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> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/galaxyproject/tools-devteam/commit/2035dc21f4c3d2a4a12b40b4cbe65714fe06f362" class="message" data-pjax="true" title="added test and test files">added test and test files</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time datetime="2014-12-01T15:45:35Z" is="time-ago">Dec 1, 2014</time></span> - </td> - </tr> - <tr> - <td class="icon"> - <span class="octicon octicon-file-text"></span> - <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" /> - </td> - <td class="content"> - <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> - </td> - <td class="message"> - <span class="css-truncate css-truncate-target"> - <a href="/galaxyproject/tools-devteam/commit/d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f" class="message" data-pjax="true" title="Unify and collectionify read group handling. - -The reusable macro file has: - - - Defines widgets for common read group parameters. - - 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). - - The conditional (used by mappers) has fours modes: - - Set according the specification (only ID required - has all parameters). Current BWA approach. - - 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``. - - 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?) - - Do not set read groups. - - Utilities for conditionally including parameters and formatting them (eliminates many explicit conditionals in the mappers for instance). - - An example "mapper" test tool which demonstrates optionally including read groups. - - An example read group assign test tool which demonstrates unconditionally specifying macros. - -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. - -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. - -Updates from original version: - - - Tests pass for ``picard_AddOrReplaceReadGroups`` as well as the BWA and Bowtie tools. - - Remove the changes from tophat - it will require more work (it is less free form and won't accept certain valid read groups arguments). - - Deleted empty lines I had previously introduced and idented the Cheetah code (hadn't realized I could do that). - -Smaller Notes: - -The new approach for BWA tools excludes empty read groups instead of adding them as empty - hopefully this is fine: - -``` --@RG ID:rg1 SM: PL:CAPILLARY --@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 -+@RG ID:rg1 PL:CAPILLARY -+@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 -```">Unify and collectionify read group handling.</a> - </span> - </td> - <td class="age"> - <span class="css-truncate css-truncate-target"><time datetime="2015-05-07T19:31:09Z" is="time-ago">May 7, 2015</time></span> - </td> - </tr> - </tbody> - </table> - -</div> - - - - - - </div> - </div> - <div class="modal-backdrop"></div> - </div> - </div> - - - </div><!-- /.wrapper --> - - <div class="container"> - <div class="site-footer" role="contentinfo"> - <ul class="site-footer-links right"> - <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> - <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> - <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li> - - </ul> - - <a href="https://github.com" aria-label="Homepage"> - <span class="mega-octicon octicon-mark-github" title="GitHub"></span> -</a> - <ul class="site-footer-links"> - <li>© 2015 <span title="0.06882s from github-fe127-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> - <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> - <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> - <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> - <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li> - </ul> - </div> -</div> - - - <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> - <div class="fullscreen-container js-suggester-container"> - <div class="textarea-wrap"> - <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder="" aria-label=""></textarea> - <div class="suggester-container"> - <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div> - </div> - </div> - </div> - <div class="fullscreen-sidebar"> - <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> - <span class="mega-octicon octicon-screen-normal"></span> - </a> - <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" - aria-label="Switch themes"> - <span class="octicon octicon-color-mode"></span> - </a> - </div> -</div> - - - - - - - <div id="ajax-error-message" class="flash flash-error"> - <span class="octicon octicon-alert"></span> - <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> - Something went wrong with that request. Please try again. - </div> - - - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-eedcd4970c51d77d26b12825fc1fb1fbd554a880c0a8649a9cac6b63f1ee7cff.js"></script> - <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github/index-1af8eb3fd83c34afcee37eae4704e57d3bb35ccacee5574545665527ae02d731.js"></script> - - - </body> -</html> -