Mercurial > repos > devteam > samtools_sort
changeset 0:4cafbe1d2ea6
initial commit
| author | martenson <cech.marten@gmail.com> |
|---|---|
| date | Wed, 10 Sep 2014 23:06:15 -0400 |
| parents | |
| children | a7b6e385a895 |
| files | samtools_sort.xml test-data/1.bam test-data/1_sort.bam tool_dependencies.xml |
| diffstat | 4 files changed, 2980 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_sort.xml Wed Sep 10 23:06:15 2014 -0400 @@ -0,0 +1,899 @@ + + + + +<!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"> + + + <title>galaxytools/samtools_sort.xml at master · bgruening/galaxytools</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="bgruening/galaxytools" name="twitter:title" /><meta content="galaxytools - Galaxy Tool wrappers" name="twitter:description" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" name="twitter:image:src" /> +<meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" property="og:image" /><meta content="bgruening/galaxytools" property="og:title" /><meta content="https://github.com/bgruening/galaxytools" property="og:url" /><meta content="galaxytools - Galaxy Tool wrappers" property="og:description" /> + + <meta name="browser-stats-url" content="/_stats"> + <link rel="assets" href="https://assets-cdn.github.com/"> + <link rel="conduit-xhr" href="https://ghconduit.com:25035"> + <link rel="xhr-socket" href="/_sockets"> + + <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="473A4A01:275A:168F6DF:5411115C" name="octolytics-dimension-request_id" /><meta content="1814954" name="octolytics-actor-id" /><meta content="martenson" name="octolytics-actor-login" /><meta content="dde9ac06cabe96d1758902d5ea67b8d45f8cc402318d8a310a5cb1697f328405" name="octolytics-actor-hash" /> + <meta content="Rails, view, blob#show" name="analytics-event" /> + + + + <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico"> + + + <meta content="authenticity_token" name="csrf-param" /> +<meta content="Ty9tf2sicVJdtF2CuUPIw4ak+iNsc1r46aMmYrLSrkd1pKVhXVQ9tfCeihWeH4ML87U5inqYaJJMSuTlVKPF3w==" name="csrf-token" /> + + <link href="https://assets-cdn.github.com/assets/github-e98a2e283e3419aa85768affc5929842870bc5fc.css" media="all" rel="stylesheet" type="text/css" /> + <link href="https://assets-cdn.github.com/assets/github2-c63e67d784fa7ee064d9610f2d22cdf8d0d7f467.css" media="all" rel="stylesheet" type="text/css" /> + + + + <meta http-equiv="x-pjax-version" content="37f365d9c8bc52a9b54820d2549e77db"> + + + <meta name="description" content="galaxytools - Galaxy Tool wrappers"> + <meta name="go-import" content="github.com/bgruening/galaxytools git https://github.com/bgruening/galaxytools.git"> + + <meta content="469983" name="octolytics-dimension-user_id" /><meta content="bgruening" name="octolytics-dimension-user_login" /><meta content="6942323" name="octolytics-dimension-repository_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="6942323" name="octolytics-dimension-repository_network_root_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_network_root_nwo" /> + <link href="https://github.com/bgruening/galaxytools/commits/master.atom" rel="alternate" title="Recent Commits to galaxytools:master" type="application/atom+xml"> + + </head> + + + <body class="logged_in env-production macintosh vis-public page-blob"> + <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"> + <div class="container clearfix"> + + <a class="header-logo-invertocat" href="https://github.com/" aria-label="Homepage" ga-data-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"> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/bgruening/galaxytools/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> + <input type="text" + class="js-site-search-field is-clearable" + data-hotkey="s" + name="q" + placeholder="Search" + data-global-scope-placeholder="Search GitHub" + data-repo-scope-placeholder="Search" + tabindex="1" + autocapitalize="off"> + <div class="scope-badge">This repository</div> +</form> + </div> + <ul class="header-nav left"> + <li class="header-nav-item explore"> + <a class="header-nav-link" href="/explore" data-ga-click="Header, go to explore, text:explore">Explore</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> + <li class="header-nav-item"> + <a class="header-nav-link" href="/blog" data-ga-click="Header, go to blog, text:blog">Blog</a> + </li> + <li class="header-nav-item"> + <a class="header-nav-link" href="https://help.github.com" data-ga-click="Header, go to help, text:help">Help</a> + </li> + </ul> + + +<ul class="header-nav user-nav right" id="user-links"> + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link name" href="/martenson" data-ga-click="Header, go to profile, text:username"> + <img alt="Marten" class="avatar" data-user="1814954" height="20" src="https://avatars1.githubusercontent.com/u/1814954?v=2&s=40" width="20" /> + <span class="css-truncate"> + <span class="css-truncate-target">martenson</span> + </span> + </a> + </li> + + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link js-menu-target tooltipped tooltipped-s" href="#" aria-label="Create new..." data-ga-click="Header, create new, icon:add"> + <span class="octicon octicon-plus"></span> + <span class="dropdown-caret"></span> + </a> + + <div class="dropdown-menu-content js-menu-content"> + +<ul class="dropdown-menu"> + <li> + <a href="/new"><span class="octicon octicon-repo"></span> New repository</a> + </li> + <li> + <a href="/organizations/new"><span class="octicon octicon-organization"></span> New organization</a> + </li> + + + <li class="dropdown-divider"></li> + <li class="dropdown-header"> + <span title="bgruening/galaxytools">This repository</span> + </li> + <li> + <a href="/bgruening/galaxytools/issues/new"><span class="octicon octicon-issue-opened"></span> New issue</a> + </li> +</ul> + + </div> + </li> + + <li class="header-nav-item"> + <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> + </li> + + <li class="header-nav-item"> + <a class="header-nav-link tooltipped tooltipped-s" href="/settings/profile" id="account_settings" aria-label="Settings" data-ga-click="Header, go to settings, icon:settings"> + <span class="octicon octicon-gear"></span> + </a> + </li> + + <li class="header-nav-item"> + <form accept-charset="UTF-8" action="/logout" class="logout-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="JmoHD8AuqFtwovPzUZGIZV+JkiupqKzpcox2nVexpunrzar6iFKMizQy6MEnyPU1gggJ28xGDE3tmZ5Vccn00g==" /></div> + <button class="header-nav-link sign-out-button tooltipped tooltipped-s" aria-label="Sign out" data-ga-click="Header, sign out, icon:logout"> + <span class="octicon octicon-sign-out"></span> + </button> +</form> </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"> + +<ul class="pagehead-actions"> + + <li class="subscription"> + <form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" 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="fMaqL7Kp35ooqsGLeroGbkRXZdvcR/Ud+D9LU+AoLA9v9NNB0RoFhGB+jF+UG/7CFaz7anex6nulIQ7dLj81mQ==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="6942323" /> + + <div class="select-menu js-menu-container js-select-menu"> + <a class="social-count js-social-count" href="/bgruening/galaxytools/watchers"> + 18 + </a> + <a href="/bgruening/galaxytools/subscription" + class="minibutton select-menu-button with-count js-menu-target" role="button" tabindex="0" aria-haspopup="true"> + <span class="js-select-button"> + <span class="octicon octicon-eye"></span> + Watch + </span> + </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> <!-- /.select-menu-header --> + + <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" /> + <h4>Not watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Ignoring</h4> + <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> <!-- /.select-menu-item --> + + </div> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> + </div> <!-- /.select-menu --> + +</form> + </li> + + <li> + + <div class="js-toggler-container js-social-container starring-container on"> + + <form accept-charset="UTF-8" action="/bgruening/galaxytools/unstar" class="js-toggler-form starred js-unstar-button" 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="WdgMeXIjssImw51FieAml78d+6cYa/yjGiW4pnh85xdDzRTSsXfBdRUFyp7YPWk9E4Qk6UYawjSNJ1PH+IxnOg==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Unstar this repository" title="Unstar bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Unstar + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/star" class="js-toggler-form unstarred js-star-button" 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="p3NWhH6b56GUJWoobNdalnehY7EfoKfOxt7yTeqNsweU2MXvu0HUFbklxPN23kuCJwxPj+nCwsW/CoBmKErn6Q==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Star this repository" title="Star bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Star + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> </div> + + </li> + + + <li> + <a href="/bgruening/galaxytools/fork" class="minibutton with-count js-toggler-target fork-button tooltipped-n" title="Fork your own copy of bgruening/galaxytools to your account" aria-label="Fork your own copy of bgruening/galaxytools to your account" rel="nofollow" data-method="post"> + <span class="octicon octicon-repo-forked"></span> + Fork + </a> + <a href="/bgruening/galaxytools/network" class="social-count">22</a> + </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="/bgruening" class="url fn" itemprop="url" rel="author"><span itemprop="title">bgruening</span></a></span><!-- + --><span class="path-divider">/</span><!-- + --><strong><a href="/bgruening/galaxytools" class="js-current-repository js-repo-home-link">galaxytools</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><!-- /.container --> + </div><!-- /.repohead --> + + <div class="container"> + <div class="repository-with-sidebar repo-container new-discussion-timeline "> + <div class="repository-sidebar clearfix"> + +<div class="sunken-menu vertical-right repo-nav js-repo-nav js-repository-container-pjax js-octicon-loaders" data-issue-count-url="/bgruening/galaxytools/issues/counts"> + <div class="sunken-menu-contents"> + <ul class="sunken-menu-group"> + <li class="tooltipped tooltipped-w" aria-label="Code"> + <a href="/bgruening/galaxytools" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-pjax="true" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /bgruening/galaxytools"> + <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="/bgruening/galaxytools/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /bgruening/galaxytools/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="/bgruening/galaxytools/pulls" aria-label="Pull Requests" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g p" data-selected-links="repo_pulls /bgruening/galaxytools/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="/bgruening/galaxytools/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g w" data-selected-links="repo_wiki /bgruening/galaxytools/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="/bgruening/galaxytools/pulse/weekly" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="pulse /bgruening/galaxytools/pulse/weekly"> + <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="/bgruening/galaxytools/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="repo_graphs repo_contributors /bgruening/galaxytools/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> + + + </div> +</div> + + <div class="only-with-full-nav"> + + +<div class="clone-url open" + data-protocol-type="http" + data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone"> + <h3><span class="text-emphasized">HTTPS</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="ssh" + data-url="/users/set_protocol?protocol_selector=ssh&protocol_type=clone"> + <h3><span class="text-emphasized">SSH</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="git@github.com:bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="git@github.com:bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="subversion" + data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone"> + <h3><span class="text-emphasized">Subversion</span> checkout URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<p class="clone-options">You can clone with + <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a>, + <a href="#" class="js-clone-selector" data-protocol="ssh">SSH</a>, + or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>. + <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> +</p> + + <a href="http://mac.github.com" data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools" class="minibutton sidebar-button js-conduit-rewrite-url" title="Save bgruening/galaxytools to your computer and use it in GitHub Desktop." aria-label="Save bgruening/galaxytools to your computer and use it in GitHub Desktop."> + <span class="octicon octicon-device-desktop"></span> + Clone in Desktop + </a> + + + <a href="/bgruening/galaxytools/archive/master.zip" + class="minibutton sidebar-button" + aria-label="Download the contents of bgruening/galaxytools as a zip file" + title="Download the contents of bgruening/galaxytools as a zip file" + rel="nofollow"> + <span class="octicon octicon-cloud-download"></span> + Download ZIP + </a> + </div> + </div><!-- /.repository-sidebar --> + + <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container> + + +<a href="/bgruening/galaxytools/blob/3a57ada6062aa513010b1bc15048135d4207f337/samtools_sort/samtools_sort.xml" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a> + +<!-- blob contrib key: blob_contributors:v21:f40ff95d19e5c54ca033554fe611f373 --> + +<div class="file-navigation"> + +<div class="select-menu js-menu-container js-select-menu left"> + <span class="minibutton select-menu-button js-menu-target css-truncate" data-hotkey="w" + data-master-branch="master" + data-ref="master" + title="master" + role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true"> + <span class="octicon octicon-git-branch"></span> + <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> <!-- /.select-menu-header --> + + <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" class="js-select-menu-tab">Branches</a> + </li> + <li class="select-menu-tab"> + <a href="#" data-tab-filter="tags" class="js-select-menu-tab">Tags</a> + </li> + </ul> + </div><!-- /.select-menu-tabs --> + </div><!-- /.select-menu-filters --> + + <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches"> + + <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> + + + <div class="select-menu-item js-navigation-item "> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/gh-pages/samtools_sort/samtools_sort.xml" + data-name="gh-pages" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="gh-pages">gh-pages</a> + </div> <!-- /.select-menu-item --> + <div class="select-menu-item js-navigation-item selected"> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/master/samtools_sort/samtools_sort.xml" + data-name="master" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="master">master</a> + </div> <!-- /.select-menu-item --> + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> <!-- /.select-menu-list --> + + <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> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> +</div> <!-- /.select-menu --> + + <div class="button-group right"> + <a href="/bgruening/galaxytools/find/master" + class="js-show-file-finder minibutton empty-icon tooltipped tooltipped-s" + data-pjax + data-hotkey="t" + aria-label="Quickly jump between files"> + <span class="octicon octicon-list-unordered"></span> + </a> + <button class="js-zeroclipboard minibutton zeroclipboard-button" + data-clipboard-text="samtools_sort/samtools_sort.xml" + aria-label="Copy to clipboard" + data-copied-hint="Copied!"> + <span class="octicon octicon-clippy"></span> + </button> + </div> + + <div class="breadcrumb"> + <span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">galaxytools</span></a></span></span><span class="separator"> / </span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools/tree/master/samtools_sort" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">samtools_sort</span></a></span><span class="separator"> / </span><strong class="final-path">samtools_sort.xml</strong> + </div> +</div> + + + <div class="commit file-history-tease"> + <div class="file-history-tease-header"> + <img alt="Björn Grüning" class="avatar" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" /> + <span class="author"><a href="/bgruening" rel="author">bgruening</a></span> + <time datetime="2014-06-23T10:59:43+02:00" is="relative-time">June 23, 2014</time> + <div class="commit-title"> + <a href="/bgruening/galaxytools/commit/3314eedb2e44d2c4b481c1f274ac27e03b8760c5" class="message" data-pjax="true" title="add new test data">add new test data</a> + </div> + </div> + + <div class="participation"> + <p class="quickstat"> + <a href="#blob_contributors_box" rel="facebox"> + <strong>1</strong> + contributor + </a> + </p> + + </div> + <div id="blob_contributors_box" style="display:none"> + <h2 class="facebox-header">Users who have contributed to this file</h2> + <ul class="facebox-user-list"> + <li class="facebox-user-list-item"> + <img alt="Björn Grüning" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" /> + <a href="/bgruening">bgruening</a> + </li> + </ul> + </div> + </div> + +<div class="file-box"> + <div class="file"> + <div class="meta clearfix"> + <div class="info file-name"> + <span>48 lines (39 sloc)</span> + <span class="meta-divider"></span> + <span>1.653 kb</span> + </div> + <div class="actions"> + <div class="button-group"> + <a href="/bgruening/galaxytools/raw/master/samtools_sort/samtools_sort.xml" class="minibutton " id="raw-url">Raw</a> + <a href="/bgruening/galaxytools/blame/master/samtools_sort/samtools_sort.xml" class="minibutton js-update-url-with-hash">Blame</a> + <a href="/bgruening/galaxytools/commits/master/samtools_sort/samtools_sort.xml" class="minibutton " rel="nofollow">History</a> + </div><!-- /.button-group --> + + <a class="octicon-button tooltipped tooltipped-nw js-conduit-openfile-check" + href="http://mac.github.com" + data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools?branch=master&filepath=samtools_sort%2Fsamtools_sort.xml" + aria-label="Open this file in GitHub for Mac" + data-failed-title="Your version of GitHub for Mac is too old to open this file. Try checking for updates."> + <span class="octicon octicon-device-desktop"></span> + </a> + + <a class="octicon-button tooltipped tooltipped-n js-update-url-with-hash" + aria-label="Clicking this button will fork this project so you can edit the file" + href="/bgruening/galaxytools/edit/master/samtools_sort/samtools_sort.xml" + data-method="post" rel="nofollow"><span class="octicon octicon-pencil"></span></a> + + <a class="octicon-button danger tooltipped tooltipped-s" + href="/bgruening/galaxytools/delete/master/samtools_sort/samtools_sort.xml" + aria-label="Fork this project and delete file" + data-method="post" data-test-id="delete-blob-file" rel="nofollow"> + <span class="octicon octicon-trashcan"></span> + </a> + </div><!-- /.actions --> + </div> + + <div class="blob-wrapper data type-xml"> + <table class="highlight tab-size-8 js-file-line-container"> + <tr> + <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> + <td id="LC1" class="blob-code js-file-line"><span class="nt"><tool</span> <span class="na">id=</span><span class="s">"samtools_sort"</span> <span class="na">name=</span><span class="s">"sort"</span> <span class="na">version=</span><span class="s">"1.0.2"</span><span class="nt">></span></td> + </tr> + <tr> + <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> + <td id="LC2" class="blob-code js-file-line"> <span class="nt"><requirements></span></td> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code js-file-line"> <span class="nt"><requirement</span> <span class="na">type=</span><span class="s">"package"</span> <span class="na">version=</span><span class="s">"0.1.19"</span><span class="nt">></span>samtools<span class="nt"></requirement></span></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code js-file-line"> <span class="nt"></requirements></span></td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code js-file-line"> <span class="nt"><description></span>a BAM file<span class="nt"></description></span></td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code js-file-line"> <span class="nt"><command></span></td> + </tr> + <tr> + <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> + <td id="LC7" class="blob-code js-file-line"> samtools sort</td> + </tr> + <tr> + <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> + <td id="LC8" class="blob-code js-file-line"> $sort_mode</td> + </tr> + <tr> + <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> + <td id="LC9" class="blob-code js-file-line"> "${input1}" foo</td> + </tr> + <tr> + <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> + <td id="LC10" class="blob-code js-file-line"> 2<span class="ni">&gt;&amp;</span>1 || echo "Error running samtools sort." <span class="ni">&gt;&amp;</span>2</td> + </tr> + <tr> + <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> + <td id="LC11" class="blob-code js-file-line"> ;</td> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code js-file-line"> mv foo.bam "${output1}"</td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code js-file-line"> <span class="nt"></command></span></td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code js-file-line"> <span class="nt"><inputs></span></td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"input1"</span> <span class="na">type=</span><span class="s">"data"</span> <span class="na">format=</span><span class="s">"bam"</span> <span class="na">label=</span><span class="s">"BAM File"</span> <span class="nt">/></span></td> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"sort_mode"</span> <span class="na">type=</span><span class="s">"select"</span> <span class="na">label=</span><span class="s">"Sort by "</span><span class="nt">></span></td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code js-file-line"> <span class="nt"><option</span> <span class="na">value=</span><span class="s">""</span> <span class="na">selected=</span><span class="s">"True"</span><span class="nt">></span>Chromosomal coordinates<span class="nt"></option></span></td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code js-file-line"> <span class="nt"><option</span> <span class="na">value=</span><span class="s">"-n"</span><span class="nt">></span>Read names<span class="nt"></option></span></td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code js-file-line"> <span class="nt"></param></span></td> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code js-file-line"> <span class="nt"></inputs></span></td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code js-file-line"> <span class="nt"><outputs></span></td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code js-file-line"> <span class="nt"><data</span> <span class="na">name=</span><span class="s">"output1"</span> <span class="na">format=</span><span class="s">"bam"</span> <span class="nt">/></span></td> + </tr> + <tr> + <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> + <td id="LC23" class="blob-code js-file-line"> <span class="nt"></outputs></span></td> + </tr> + <tr> + <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> + <td id="LC24" class="blob-code js-file-line"> <span class="nt"><tests></span></td> + </tr> + <tr> + <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> + <td id="LC25" class="blob-code js-file-line"> <span class="nt"><test></span></td> + </tr> + <tr> + <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> + <td id="LC26" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"input1"</span> <span class="na">value=</span><span class="s">"1.bam"</span> <span class="na">ftype=</span><span class="s">"bam"</span> <span class="nt">/></span></td> + </tr> + <tr> + <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> + <td id="LC27" class="blob-code js-file-line"> <span class="nt"><output</span> <span class="na">name=</span><span class="s">"output1"</span> <span class="na">file=</span><span class="s">"1_sort.bam"</span> <span class="na">ftype=</span><span class="s">"bam"</span> <span class="na">sort=</span><span class="s">"True"</span><span class="nt">/></span></td> + </tr> + <tr> + <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> + <td id="LC28" class="blob-code js-file-line"> <span class="nt"></test></span></td> + </tr> + <tr> + <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> + <td id="LC29" class="blob-code js-file-line"> <span class="nt"></tests></span></td> + </tr> + <tr> + <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> + <td id="LC30" class="blob-code js-file-line"> <span class="nt"><help></span></td> + </tr> + <tr> + <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> + <td id="LC31" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> + <td id="LC32" class="blob-code js-file-line">**What it does**</td> + </tr> + <tr> + <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> + <td id="LC33" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> + <td id="LC34" class="blob-code js-file-line">This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.</td> + </tr> + <tr> + <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> + <td id="LC35" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> + <td id="LC36" class="blob-code js-file-line">.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml</td> + </tr> + <tr> + <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> + <td id="LC37" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> + <td id="LC38" class="blob-code js-file-line">------</td> + </tr> + <tr> + <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> + <td id="LC39" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> + <td id="LC40" class="blob-code js-file-line">**Citation**</td> + </tr> + <tr> + <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> + <td id="LC41" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> + <td id="LC42" class="blob-code js-file-line">For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <span class="ni">&lt;</span>http://www.ncbi.nlm.nih.gov/pubmed/19505943<span class="ni">&gt;</span>`_</td> + </tr> + <tr> + <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> + <td id="LC43" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> + <td id="LC44" class="blob-code js-file-line">If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*</td> + </tr> + <tr> + <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> + <td id="LC45" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> + <td id="LC46" class="blob-code js-file-line"> <span class="nt"></help></span></td> + </tr> + <tr> + <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> + <td id="LC47" class="blob-code js-file-line"><span class="nt"></tool></span></td> + </tr> +</table> + + </div> + + </div> +</div> + +<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> +<div id="jump-to-line" style="display:none"> + <form accept-charset="UTF-8" class="js-jump-to-line-form"> + <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> + <button type="submit" class="button">Go</button> + </form> +</div> + + </div> + + </div><!-- /.repo-container --> + <div class="modal-backdrop"></div> + </div><!-- /.container --> + </div><!-- /.site --> + + + </div><!-- /.wrapper --> + + <div class="container"> + <div class="site-footer"> + <ul class="site-footer-links right"> + <li><a href="https://status.github.com/">Status</a></li> + <li><a href="http://developer.github.com">API</a></li> + <li><a href="http://training.github.com">Training</a></li> + <li><a href="http://shop.github.com">Shop</a></li> + <li><a href="/blog">Blog</a></li> + <li><a href="/about">About</a></li> + + </ul> + + <a href="/" aria-label="Homepage"> + <span class="mega-octicon octicon-mark-github" title="GitHub"></span> + </a> + + <ul class="site-footer-links"> + <li>© 2014 <span title="0.04104s from github-fe135-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> + <li><a href="/site/terms">Terms</a></li> + <li><a href="/site/privacy">Privacy</a></li> + <li><a href="/security">Security</a></li> + <li><a href="/contact">Contact</a></li> + </ul> + </div><!-- /.site-footer --> +</div><!-- /.container --> + + + <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 js-suggester-field" placeholder=""></textarea> + </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-0c1b00f7935ae85624f5fc5d40d52d60febf92b4.js" type="text/javascript"></script> + <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-cbba41b870c9e4d89d40771e5c675b37b14e9601.js" type="text/javascript"></script> + + + <script async src="https://www.google-analytics.com/analytics.js"></script> + </body> +</html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bam Wed Sep 10 23:06:15 2014 -0400 @@ -0,0 +1,677 @@ + + + + +<!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"> + + + <title>galaxytools/1.bam at master · bgruening/galaxytools</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="bgruening/galaxytools" name="twitter:title" /><meta content="galaxytools - Galaxy Tool wrappers" name="twitter:description" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" name="twitter:image:src" /> +<meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" property="og:image" /><meta content="bgruening/galaxytools" property="og:title" /><meta content="https://github.com/bgruening/galaxytools" property="og:url" /><meta content="galaxytools - Galaxy Tool wrappers" property="og:description" /> + + <meta name="browser-stats-url" content="/_stats"> + <link rel="assets" href="https://assets-cdn.github.com/"> + <link rel="conduit-xhr" href="https://ghconduit.com:25035"> + <link rel="xhr-socket" href="/_sockets"> + + <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="473A4A01:275A:168FAE8:54111161" name="octolytics-dimension-request_id" /><meta content="1814954" name="octolytics-actor-id" /><meta content="martenson" name="octolytics-actor-login" /><meta content="dde9ac06cabe96d1758902d5ea67b8d45f8cc402318d8a310a5cb1697f328405" name="octolytics-actor-hash" /> + <meta content="Rails, view, blob#show" name="analytics-event" /> + + + + <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico"> + + + <meta content="authenticity_token" name="csrf-param" /> +<meta content="e/po+/l13qw1RdQD44fDo8VJsj5g7HrHRh/+1Ue13oiFwRxWUSk4gscJlnrn41ZbA3IejErxP31Q5EljuVTHXQ==" name="csrf-token" /> + + <link href="https://assets-cdn.github.com/assets/github-e98a2e283e3419aa85768affc5929842870bc5fc.css" media="all" rel="stylesheet" type="text/css" /> + <link href="https://assets-cdn.github.com/assets/github2-c63e67d784fa7ee064d9610f2d22cdf8d0d7f467.css" media="all" rel="stylesheet" type="text/css" /> + + + + <meta http-equiv="x-pjax-version" content="37f365d9c8bc52a9b54820d2549e77db"> + + + <meta name="description" content="galaxytools - Galaxy Tool wrappers"> + <meta name="go-import" content="github.com/bgruening/galaxytools git https://github.com/bgruening/galaxytools.git"> + + <meta content="469983" name="octolytics-dimension-user_id" /><meta content="bgruening" name="octolytics-dimension-user_login" /><meta content="6942323" name="octolytics-dimension-repository_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="6942323" name="octolytics-dimension-repository_network_root_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_network_root_nwo" /> + <link href="https://github.com/bgruening/galaxytools/commits/master.atom" rel="alternate" title="Recent Commits to galaxytools:master" type="application/atom+xml"> + + </head> + + + <body class="logged_in env-production macintosh vis-public page-blob"> + <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"> + <div class="container clearfix"> + + <a class="header-logo-invertocat" href="https://github.com/" aria-label="Homepage" ga-data-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"> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/bgruening/galaxytools/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> + <input type="text" + class="js-site-search-field is-clearable" + data-hotkey="s" + name="q" + placeholder="Search" + data-global-scope-placeholder="Search GitHub" + data-repo-scope-placeholder="Search" + tabindex="1" + autocapitalize="off"> + <div class="scope-badge">This repository</div> +</form> + </div> + <ul class="header-nav left"> + <li class="header-nav-item explore"> + <a class="header-nav-link" href="/explore" data-ga-click="Header, go to explore, text:explore">Explore</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> + <li class="header-nav-item"> + <a class="header-nav-link" href="/blog" data-ga-click="Header, go to blog, text:blog">Blog</a> + </li> + <li class="header-nav-item"> + <a class="header-nav-link" href="https://help.github.com" data-ga-click="Header, go to help, text:help">Help</a> + </li> + </ul> + + +<ul class="header-nav user-nav right" id="user-links"> + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link name" href="/martenson" data-ga-click="Header, go to profile, text:username"> + <img alt="Marten" class="avatar" data-user="1814954" height="20" src="https://avatars1.githubusercontent.com/u/1814954?v=2&s=40" width="20" /> + <span class="css-truncate"> + <span class="css-truncate-target">martenson</span> + </span> + </a> + </li> + + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link js-menu-target tooltipped tooltipped-s" href="#" aria-label="Create new..." data-ga-click="Header, create new, icon:add"> + <span class="octicon octicon-plus"></span> + <span class="dropdown-caret"></span> + </a> + + <div class="dropdown-menu-content js-menu-content"> + +<ul class="dropdown-menu"> + <li> + <a href="/new"><span class="octicon octicon-repo"></span> New repository</a> + </li> + <li> + <a href="/organizations/new"><span class="octicon octicon-organization"></span> New organization</a> + </li> + + + <li class="dropdown-divider"></li> + <li class="dropdown-header"> + <span title="bgruening/galaxytools">This repository</span> + </li> + <li> + <a href="/bgruening/galaxytools/issues/new"><span class="octicon octicon-issue-opened"></span> New issue</a> + </li> +</ul> + + </div> + </li> + + <li class="header-nav-item"> + <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> + </li> + + <li class="header-nav-item"> + <a class="header-nav-link tooltipped tooltipped-s" href="/settings/profile" id="account_settings" aria-label="Settings" data-ga-click="Header, go to settings, icon:settings"> + <span class="octicon octicon-gear"></span> + </a> + </li> + + <li class="header-nav-item"> + <form accept-charset="UTF-8" action="/logout" class="logout-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="NzkdsDLfeT4a64PQx4j3B7Sf5GGdO8VeIcXWwQSlOlPaB2GjHeph/uYMpoTfZ8ab3QNJLIROIevfBAbM9RgttA==" /></div> + <button class="header-nav-link sign-out-button tooltipped tooltipped-s" aria-label="Sign out" data-ga-click="Header, sign out, icon:logout"> + <span class="octicon octicon-sign-out"></span> + </button> +</form> </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"> + +<ul class="pagehead-actions"> + + <li class="subscription"> + <form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" 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="02SnxhR2K3xw3On7N4Xa5X6FecQsLPBr/ebUTSWXG4bJZ4F2Qdt07Fcx1omyGSVHJWkSf1kDEk66MeMk+vv09g==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="6942323" /> + + <div class="select-menu js-menu-container js-select-menu"> + <a class="social-count js-social-count" href="/bgruening/galaxytools/watchers"> + 18 + </a> + <a href="/bgruening/galaxytools/subscription" + class="minibutton select-menu-button with-count js-menu-target" role="button" tabindex="0" aria-haspopup="true"> + <span class="js-select-button"> + <span class="octicon octicon-eye"></span> + Watch + </span> + </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> <!-- /.select-menu-header --> + + <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" /> + <h4>Not watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Ignoring</h4> + <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> <!-- /.select-menu-item --> + + </div> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> + </div> <!-- /.select-menu --> + +</form> + </li> + + <li> + + <div class="js-toggler-container js-social-container starring-container on"> + + <form accept-charset="UTF-8" action="/bgruening/galaxytools/unstar" class="js-toggler-form starred js-unstar-button" 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="OkB8VOG5D9GOuAv/3N5ACw0Wbx6boPWGp7v0UXxJz6mvRDAUxHp/F+wjWiLvOIYpbwfuIiVzQj9zeTVprn+dFw==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Unstar this repository" title="Unstar bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Unstar + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/star" class="js-toggler-form unstarred js-star-button" 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="tLiPR01TBugEEpxrmnGopJk4XCODnKU/26yQ5fZQm5Kb8B5d4c0VaCTo7cgusG/nL82E3fnhStUCP+2He4bsJQ==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Star this repository" title="Star bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Star + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> </div> + + </li> + + + <li> + <a href="/bgruening/galaxytools/fork" class="minibutton with-count js-toggler-target fork-button tooltipped-n" title="Fork your own copy of bgruening/galaxytools to your account" aria-label="Fork your own copy of bgruening/galaxytools to your account" rel="nofollow" data-method="post"> + <span class="octicon octicon-repo-forked"></span> + Fork + </a> + <a href="/bgruening/galaxytools/network" class="social-count">22</a> + </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="/bgruening" class="url fn" itemprop="url" rel="author"><span itemprop="title">bgruening</span></a></span><!-- + --><span class="path-divider">/</span><!-- + --><strong><a href="/bgruening/galaxytools" class="js-current-repository js-repo-home-link">galaxytools</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><!-- /.container --> + </div><!-- /.repohead --> + + <div class="container"> + <div class="repository-with-sidebar repo-container new-discussion-timeline "> + <div class="repository-sidebar clearfix"> + +<div class="sunken-menu vertical-right repo-nav js-repo-nav js-repository-container-pjax js-octicon-loaders" data-issue-count-url="/bgruening/galaxytools/issues/counts"> + <div class="sunken-menu-contents"> + <ul class="sunken-menu-group"> + <li class="tooltipped tooltipped-w" aria-label="Code"> + <a href="/bgruening/galaxytools" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-pjax="true" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /bgruening/galaxytools"> + <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="/bgruening/galaxytools/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /bgruening/galaxytools/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="/bgruening/galaxytools/pulls" aria-label="Pull Requests" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g p" data-selected-links="repo_pulls /bgruening/galaxytools/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="/bgruening/galaxytools/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g w" data-selected-links="repo_wiki /bgruening/galaxytools/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="/bgruening/galaxytools/pulse/weekly" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="pulse /bgruening/galaxytools/pulse/weekly"> + <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="/bgruening/galaxytools/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="repo_graphs repo_contributors /bgruening/galaxytools/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> + + + </div> +</div> + + <div class="only-with-full-nav"> + + +<div class="clone-url open" + data-protocol-type="http" + data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone"> + <h3><span class="text-emphasized">HTTPS</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="ssh" + data-url="/users/set_protocol?protocol_selector=ssh&protocol_type=clone"> + <h3><span class="text-emphasized">SSH</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="git@github.com:bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="git@github.com:bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="subversion" + data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone"> + <h3><span class="text-emphasized">Subversion</span> checkout URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<p class="clone-options">You can clone with + <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a>, + <a href="#" class="js-clone-selector" data-protocol="ssh">SSH</a>, + or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>. + <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> +</p> + + <a href="http://mac.github.com" data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools" class="minibutton sidebar-button js-conduit-rewrite-url" title="Save bgruening/galaxytools to your computer and use it in GitHub Desktop." aria-label="Save bgruening/galaxytools to your computer and use it in GitHub Desktop."> + <span class="octicon octicon-device-desktop"></span> + Clone in Desktop + </a> + + + <a href="/bgruening/galaxytools/archive/master.zip" + class="minibutton sidebar-button" + aria-label="Download the contents of bgruening/galaxytools as a zip file" + title="Download the contents of bgruening/galaxytools as a zip file" + rel="nofollow"> + <span class="octicon octicon-cloud-download"></span> + Download ZIP + </a> + </div> + </div><!-- /.repository-sidebar --> + + <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container> + + +<a href="/bgruening/galaxytools/blob/3a57ada6062aa513010b1bc15048135d4207f337/samtools_sort/test-data/1.bam" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a> + +<!-- blob contrib key: blob_contributors:v21:b875a89b8ed1c27a7d5bd3948ea3ea2e --> + +<div class="file-navigation"> + +<div class="select-menu js-menu-container js-select-menu left"> + <span class="minibutton select-menu-button js-menu-target css-truncate" data-hotkey="w" + data-master-branch="master" + data-ref="master" + title="master" + role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true"> + <span class="octicon octicon-git-branch"></span> + <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> <!-- /.select-menu-header --> + + <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" class="js-select-menu-tab">Branches</a> + </li> + <li class="select-menu-tab"> + <a href="#" data-tab-filter="tags" class="js-select-menu-tab">Tags</a> + </li> + </ul> + </div><!-- /.select-menu-tabs --> + </div><!-- /.select-menu-filters --> + + <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches"> + + <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> + + + <div class="select-menu-item js-navigation-item "> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/gh-pages/samtools_sort/test-data/1.bam" + data-name="gh-pages" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="gh-pages">gh-pages</a> + </div> <!-- /.select-menu-item --> + <div class="select-menu-item js-navigation-item selected"> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/master/samtools_sort/test-data/1.bam" + data-name="master" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="master">master</a> + </div> <!-- /.select-menu-item --> + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> <!-- /.select-menu-list --> + + <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> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> +</div> <!-- /.select-menu --> + + <div class="button-group right"> + <a href="/bgruening/galaxytools/find/master" + class="js-show-file-finder minibutton empty-icon tooltipped tooltipped-s" + data-pjax + data-hotkey="t" + aria-label="Quickly jump between files"> + <span class="octicon octicon-list-unordered"></span> + </a> + <button class="js-zeroclipboard minibutton zeroclipboard-button" + data-clipboard-text="samtools_sort/test-data/1.bam" + aria-label="Copy to clipboard" + data-copied-hint="Copied!"> + <span class="octicon octicon-clippy"></span> + </button> + </div> + + <div class="breadcrumb"> + <span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">galaxytools</span></a></span></span><span class="separator"> / </span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools/tree/master/samtools_sort" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">samtools_sort</span></a></span><span class="separator"> / </span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools/tree/master/samtools_sort/test-data" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">test-data</span></a></span><span class="separator"> / </span><strong class="final-path">1.bam</strong> + </div> +</div> + + + <div class="commit commit-loader file-history-tease js-deferred-content" data-url="/bgruening/galaxytools/contributors/master/samtools_sort/test-data/1.bam"> + <div class="file-history-tease-header"> + Fetching contributors… + </div> + + <div class="participation"> + <p class="loader-loading"><img alt="" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" /></p> + <p class="loader-error">Cannot retrieve contributors at this time</p> + </div> + </div> + +<div class="file-box"> + <div class="file"> + <div class="meta clearfix"> + <div class="info file-name"> + <span>3.592 kb</span> + </div> + <div class="actions"> + <div class="button-group"> + <a href="/bgruening/galaxytools/raw/master/samtools_sort/test-data/1.bam" class="minibutton " id="raw-url">Raw</a> + <a href="/bgruening/galaxytools/commits/master/samtools_sort/test-data/1.bam" class="minibutton " rel="nofollow">History</a> + </div><!-- /.button-group --> + + <a class="octicon-button tooltipped tooltipped-nw js-conduit-openfile-check" + href="http://mac.github.com" + data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools?branch=master&filepath=samtools_sort%2Ftest-data%2F1.bam" + aria-label="Open this file in GitHub for Mac" + data-failed-title="Your version of GitHub for Mac is too old to open this file. Try checking for updates."> + <span class="octicon octicon-device-desktop"></span> + </a> + + + <a class="octicon-button danger tooltipped tooltipped-s" + href="/bgruening/galaxytools/delete/master/samtools_sort/test-data/1.bam" + aria-label="Fork this project and delete file" + data-method="post" data-test-id="delete-blob-file" rel="nofollow"> + <span class="octicon octicon-trashcan"></span> + </a> + </div><!-- /.actions --> + </div> + + <div class="blob-wrapper data type-text"> + <div class="image"> + <a href="/bgruening/galaxytools/blob/master/samtools_sort/test-data/1.bam?raw=true">View Raw</a> + </div> + </div> + + </div> +</div> + +<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> +<div id="jump-to-line" style="display:none"> + <form accept-charset="UTF-8" class="js-jump-to-line-form"> + <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> + <button type="submit" class="button">Go</button> + </form> +</div> + + </div> + + </div><!-- /.repo-container --> + <div class="modal-backdrop"></div> + </div><!-- /.container --> + </div><!-- /.site --> + + + </div><!-- /.wrapper --> + + <div class="container"> + <div class="site-footer"> + <ul class="site-footer-links right"> + <li><a href="https://status.github.com/">Status</a></li> + <li><a href="http://developer.github.com">API</a></li> + <li><a href="http://training.github.com">Training</a></li> + <li><a href="http://shop.github.com">Shop</a></li> + <li><a href="/blog">Blog</a></li> + <li><a href="/about">About</a></li> + + </ul> + + <a href="/" aria-label="Homepage"> + <span class="mega-octicon octicon-mark-github" title="GitHub"></span> + </a> + + <ul class="site-footer-links"> + <li>© 2014 <span title="0.04588s from github-fe119-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> + <li><a href="/site/terms">Terms</a></li> + <li><a href="/site/privacy">Privacy</a></li> + <li><a href="/security">Security</a></li> + <li><a href="/contact">Contact</a></li> + </ul> + </div><!-- /.site-footer --> +</div><!-- /.container --> + + + <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 js-suggester-field" placeholder=""></textarea> + </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-0c1b00f7935ae85624f5fc5d40d52d60febf92b4.js" type="text/javascript"></script> + <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-cbba41b870c9e4d89d40771e5c675b37b14e9601.js" type="text/javascript"></script> + + + <script async src="https://www.google-analytics.com/analytics.js"></script> + </body> +</html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_sort.bam Wed Sep 10 23:06:15 2014 -0400 @@ -0,0 +1,677 @@ + + + + +<!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"> + + + <title>galaxytools/1_sort.bam at master · bgruening/galaxytools</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="bgruening/galaxytools" name="twitter:title" /><meta content="galaxytools - Galaxy Tool wrappers" name="twitter:description" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" name="twitter:image:src" /> +<meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" property="og:image" /><meta content="bgruening/galaxytools" property="og:title" /><meta content="https://github.com/bgruening/galaxytools" property="og:url" /><meta content="galaxytools - Galaxy Tool wrappers" property="og:description" /> + + <meta name="browser-stats-url" content="/_stats"> + <link rel="assets" href="https://assets-cdn.github.com/"> + <link rel="conduit-xhr" href="https://ghconduit.com:25035"> + <link rel="xhr-socket" href="/_sockets"> + + <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="473A4A01:275A:168FDCA:54111164" name="octolytics-dimension-request_id" /><meta content="1814954" name="octolytics-actor-id" /><meta content="martenson" name="octolytics-actor-login" /><meta content="dde9ac06cabe96d1758902d5ea67b8d45f8cc402318d8a310a5cb1697f328405" name="octolytics-actor-hash" /> + <meta content="Rails, view, blob#show" name="analytics-event" /> + + + + <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico"> + + + <meta content="authenticity_token" name="csrf-param" /> +<meta content="NhqkPNf69u/KM31dJaKbEWU3p41xdaMu2KODrSIrOJGk3ckm3SccUIsfFR21kXgh13QxqEHkrZTTx4X9lO7pmQ==" name="csrf-token" /> + + <link href="https://assets-cdn.github.com/assets/github-e98a2e283e3419aa85768affc5929842870bc5fc.css" media="all" rel="stylesheet" type="text/css" /> + <link href="https://assets-cdn.github.com/assets/github2-c63e67d784fa7ee064d9610f2d22cdf8d0d7f467.css" media="all" rel="stylesheet" type="text/css" /> + + + + <meta http-equiv="x-pjax-version" content="37f365d9c8bc52a9b54820d2549e77db"> + + + <meta name="description" content="galaxytools - Galaxy Tool wrappers"> + <meta name="go-import" content="github.com/bgruening/galaxytools git https://github.com/bgruening/galaxytools.git"> + + <meta content="469983" name="octolytics-dimension-user_id" /><meta content="bgruening" name="octolytics-dimension-user_login" /><meta content="6942323" name="octolytics-dimension-repository_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="6942323" name="octolytics-dimension-repository_network_root_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_network_root_nwo" /> + <link href="https://github.com/bgruening/galaxytools/commits/master.atom" rel="alternate" title="Recent Commits to galaxytools:master" type="application/atom+xml"> + + </head> + + + <body class="logged_in env-production macintosh vis-public page-blob"> + <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"> + <div class="container clearfix"> + + <a class="header-logo-invertocat" href="https://github.com/" aria-label="Homepage" ga-data-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"> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/bgruening/galaxytools/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> + <input type="text" + class="js-site-search-field is-clearable" + data-hotkey="s" + name="q" + placeholder="Search" + data-global-scope-placeholder="Search GitHub" + data-repo-scope-placeholder="Search" + tabindex="1" + autocapitalize="off"> + <div class="scope-badge">This repository</div> +</form> + </div> + <ul class="header-nav left"> + <li class="header-nav-item explore"> + <a class="header-nav-link" href="/explore" data-ga-click="Header, go to explore, text:explore">Explore</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> + <li class="header-nav-item"> + <a class="header-nav-link" href="/blog" data-ga-click="Header, go to blog, text:blog">Blog</a> + </li> + <li class="header-nav-item"> + <a class="header-nav-link" href="https://help.github.com" data-ga-click="Header, go to help, text:help">Help</a> + </li> + </ul> + + +<ul class="header-nav user-nav right" id="user-links"> + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link name" href="/martenson" data-ga-click="Header, go to profile, text:username"> + <img alt="Marten" class="avatar" data-user="1814954" height="20" src="https://avatars1.githubusercontent.com/u/1814954?v=2&s=40" width="20" /> + <span class="css-truncate"> + <span class="css-truncate-target">martenson</span> + </span> + </a> + </li> + + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link js-menu-target tooltipped tooltipped-s" href="#" aria-label="Create new..." data-ga-click="Header, create new, icon:add"> + <span class="octicon octicon-plus"></span> + <span class="dropdown-caret"></span> + </a> + + <div class="dropdown-menu-content js-menu-content"> + +<ul class="dropdown-menu"> + <li> + <a href="/new"><span class="octicon octicon-repo"></span> New repository</a> + </li> + <li> + <a href="/organizations/new"><span class="octicon octicon-organization"></span> New organization</a> + </li> + + + <li class="dropdown-divider"></li> + <li class="dropdown-header"> + <span title="bgruening/galaxytools">This repository</span> + </li> + <li> + <a href="/bgruening/galaxytools/issues/new"><span class="octicon octicon-issue-opened"></span> New issue</a> + </li> +</ul> + + </div> + </li> + + <li class="header-nav-item"> + <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> + </li> + + <li class="header-nav-item"> + <a class="header-nav-link tooltipped tooltipped-s" href="/settings/profile" id="account_settings" aria-label="Settings" data-ga-click="Header, go to settings, icon:settings"> + <span class="octicon octicon-gear"></span> + </a> + </li> + + <li class="header-nav-item"> + <form accept-charset="UTF-8" action="/logout" class="logout-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="L6BP5W4W9Z+oJeRBcH4vBF3A1QdSZ2FID2NdYb7Wv4/3uBRrqGGI4z2ZIv7hZvgYtsEWptUgykl1uaM3yIXqUg==" /></div> + <button class="header-nav-link sign-out-button tooltipped tooltipped-s" aria-label="Sign out" data-ga-click="Header, sign out, icon:logout"> + <span class="octicon octicon-sign-out"></span> + </button> +</form> </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"> + +<ul class="pagehead-actions"> + + <li class="subscription"> + <form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" 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="FHVcBANTJmtM5NnuPUxYkTcwD96IkHBEc5mz5H7fQsNWymspTCZPw3mP5/oxTaKQW/foviyUeRr2Rd+/A5TMIw==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="6942323" /> + + <div class="select-menu js-menu-container js-select-menu"> + <a class="social-count js-social-count" href="/bgruening/galaxytools/watchers"> + 18 + </a> + <a href="/bgruening/galaxytools/subscription" + class="minibutton select-menu-button with-count js-menu-target" role="button" tabindex="0" aria-haspopup="true"> + <span class="js-select-button"> + <span class="octicon octicon-eye"></span> + Watch + </span> + </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> <!-- /.select-menu-header --> + + <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" /> + <h4>Not watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Ignoring</h4> + <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> <!-- /.select-menu-item --> + + </div> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> + </div> <!-- /.select-menu --> + +</form> + </li> + + <li> + + <div class="js-toggler-container js-social-container starring-container on"> + + <form accept-charset="UTF-8" action="/bgruening/galaxytools/unstar" class="js-toggler-form starred js-unstar-button" 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="Vy7np1X5m4sPSnkZoaY0N1rtbrCOuk7kQyn6IvIYX4JY6RhqZeijiQ7bsQj0wJmKQT+0NzU7WxM/GOUstOip1g==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Unstar this repository" title="Unstar bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Unstar + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/star" class="js-toggler-form unstarred js-star-button" 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="PhbWFenPrMpMBlgAxX5oz4SjpNIMd5k4jts4kaEQ7xY2m3NCNjLmGBRCMA4OtOoGJKxM3g/+kX52cbINCkrlUQ==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Star this repository" title="Star bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Star + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> </div> + + </li> + + + <li> + <a href="/bgruening/galaxytools/fork" class="minibutton with-count js-toggler-target fork-button tooltipped-n" title="Fork your own copy of bgruening/galaxytools to your account" aria-label="Fork your own copy of bgruening/galaxytools to your account" rel="nofollow" data-method="post"> + <span class="octicon octicon-repo-forked"></span> + Fork + </a> + <a href="/bgruening/galaxytools/network" class="social-count">22</a> + </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="/bgruening" class="url fn" itemprop="url" rel="author"><span itemprop="title">bgruening</span></a></span><!-- + --><span class="path-divider">/</span><!-- + --><strong><a href="/bgruening/galaxytools" class="js-current-repository js-repo-home-link">galaxytools</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><!-- /.container --> + </div><!-- /.repohead --> + + <div class="container"> + <div class="repository-with-sidebar repo-container new-discussion-timeline "> + <div class="repository-sidebar clearfix"> + +<div class="sunken-menu vertical-right repo-nav js-repo-nav js-repository-container-pjax js-octicon-loaders" data-issue-count-url="/bgruening/galaxytools/issues/counts"> + <div class="sunken-menu-contents"> + <ul class="sunken-menu-group"> + <li class="tooltipped tooltipped-w" aria-label="Code"> + <a href="/bgruening/galaxytools" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-pjax="true" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /bgruening/galaxytools"> + <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="/bgruening/galaxytools/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /bgruening/galaxytools/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="/bgruening/galaxytools/pulls" aria-label="Pull Requests" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g p" data-selected-links="repo_pulls /bgruening/galaxytools/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="/bgruening/galaxytools/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g w" data-selected-links="repo_wiki /bgruening/galaxytools/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="/bgruening/galaxytools/pulse/weekly" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="pulse /bgruening/galaxytools/pulse/weekly"> + <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="/bgruening/galaxytools/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="repo_graphs repo_contributors /bgruening/galaxytools/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> + + + </div> +</div> + + <div class="only-with-full-nav"> + + +<div class="clone-url open" + data-protocol-type="http" + data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone"> + <h3><span class="text-emphasized">HTTPS</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="ssh" + data-url="/users/set_protocol?protocol_selector=ssh&protocol_type=clone"> + <h3><span class="text-emphasized">SSH</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="git@github.com:bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="git@github.com:bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="subversion" + data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone"> + <h3><span class="text-emphasized">Subversion</span> checkout URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<p class="clone-options">You can clone with + <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a>, + <a href="#" class="js-clone-selector" data-protocol="ssh">SSH</a>, + or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>. + <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> +</p> + + <a href="http://mac.github.com" data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools" class="minibutton sidebar-button js-conduit-rewrite-url" title="Save bgruening/galaxytools to your computer and use it in GitHub Desktop." aria-label="Save bgruening/galaxytools to your computer and use it in GitHub Desktop."> + <span class="octicon octicon-device-desktop"></span> + Clone in Desktop + </a> + + + <a href="/bgruening/galaxytools/archive/master.zip" + class="minibutton sidebar-button" + aria-label="Download the contents of bgruening/galaxytools as a zip file" + title="Download the contents of bgruening/galaxytools as a zip file" + rel="nofollow"> + <span class="octicon octicon-cloud-download"></span> + Download ZIP + </a> + </div> + </div><!-- /.repository-sidebar --> + + <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container> + + +<a href="/bgruening/galaxytools/blob/3a57ada6062aa513010b1bc15048135d4207f337/samtools_sort/test-data/1_sort.bam" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a> + +<!-- blob contrib key: blob_contributors:v21:f122cca0ab5757362bdf76ee45b75705 --> + +<div class="file-navigation"> + +<div class="select-menu js-menu-container js-select-menu left"> + <span class="minibutton select-menu-button js-menu-target css-truncate" data-hotkey="w" + data-master-branch="master" + data-ref="master" + title="master" + role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true"> + <span class="octicon octicon-git-branch"></span> + <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> <!-- /.select-menu-header --> + + <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" class="js-select-menu-tab">Branches</a> + </li> + <li class="select-menu-tab"> + <a href="#" data-tab-filter="tags" class="js-select-menu-tab">Tags</a> + </li> + </ul> + </div><!-- /.select-menu-tabs --> + </div><!-- /.select-menu-filters --> + + <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches"> + + <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> + + + <div class="select-menu-item js-navigation-item "> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/gh-pages/samtools_sort/test-data/1_sort.bam" + data-name="gh-pages" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="gh-pages">gh-pages</a> + </div> <!-- /.select-menu-item --> + <div class="select-menu-item js-navigation-item selected"> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/master/samtools_sort/test-data/1_sort.bam" + data-name="master" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="master">master</a> + </div> <!-- /.select-menu-item --> + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> <!-- /.select-menu-list --> + + <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> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> +</div> <!-- /.select-menu --> + + <div class="button-group right"> + <a href="/bgruening/galaxytools/find/master" + class="js-show-file-finder minibutton empty-icon tooltipped tooltipped-s" + data-pjax + data-hotkey="t" + aria-label="Quickly jump between files"> + <span class="octicon octicon-list-unordered"></span> + </a> + <button class="js-zeroclipboard minibutton zeroclipboard-button" + data-clipboard-text="samtools_sort/test-data/1_sort.bam" + aria-label="Copy to clipboard" + data-copied-hint="Copied!"> + <span class="octicon octicon-clippy"></span> + </button> + </div> + + <div class="breadcrumb"> + <span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">galaxytools</span></a></span></span><span class="separator"> / </span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools/tree/master/samtools_sort" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">samtools_sort</span></a></span><span class="separator"> / </span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools/tree/master/samtools_sort/test-data" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">test-data</span></a></span><span class="separator"> / </span><strong class="final-path">1_sort.bam</strong> + </div> +</div> + + + <div class="commit commit-loader file-history-tease js-deferred-content" data-url="/bgruening/galaxytools/contributors/master/samtools_sort/test-data/1_sort.bam"> + <div class="file-history-tease-header"> + Fetching contributors… + </div> + + <div class="participation"> + <p class="loader-loading"><img alt="" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" /></p> + <p class="loader-error">Cannot retrieve contributors at this time</p> + </div> + </div> + +<div class="file-box"> + <div class="file"> + <div class="meta clearfix"> + <div class="info file-name"> + <span>3.491 kb</span> + </div> + <div class="actions"> + <div class="button-group"> + <a href="/bgruening/galaxytools/raw/master/samtools_sort/test-data/1_sort.bam" class="minibutton " id="raw-url">Raw</a> + <a href="/bgruening/galaxytools/commits/master/samtools_sort/test-data/1_sort.bam" class="minibutton " rel="nofollow">History</a> + </div><!-- /.button-group --> + + <a class="octicon-button tooltipped tooltipped-nw js-conduit-openfile-check" + href="http://mac.github.com" + data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools?branch=master&filepath=samtools_sort%2Ftest-data%2F1_sort.bam" + aria-label="Open this file in GitHub for Mac" + data-failed-title="Your version of GitHub for Mac is too old to open this file. Try checking for updates."> + <span class="octicon octicon-device-desktop"></span> + </a> + + + <a class="octicon-button danger tooltipped tooltipped-s" + href="/bgruening/galaxytools/delete/master/samtools_sort/test-data/1_sort.bam" + aria-label="Fork this project and delete file" + data-method="post" data-test-id="delete-blob-file" rel="nofollow"> + <span class="octicon octicon-trashcan"></span> + </a> + </div><!-- /.actions --> + </div> + + <div class="blob-wrapper data type-text"> + <div class="image"> + <a href="/bgruening/galaxytools/blob/master/samtools_sort/test-data/1_sort.bam?raw=true">View Raw</a> + </div> + </div> + + </div> +</div> + +<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> +<div id="jump-to-line" style="display:none"> + <form accept-charset="UTF-8" class="js-jump-to-line-form"> + <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> + <button type="submit" class="button">Go</button> + </form> +</div> + + </div> + + </div><!-- /.repo-container --> + <div class="modal-backdrop"></div> + </div><!-- /.container --> + </div><!-- /.site --> + + + </div><!-- /.wrapper --> + + <div class="container"> + <div class="site-footer"> + <ul class="site-footer-links right"> + <li><a href="https://status.github.com/">Status</a></li> + <li><a href="http://developer.github.com">API</a></li> + <li><a href="http://training.github.com">Training</a></li> + <li><a href="http://shop.github.com">Shop</a></li> + <li><a href="/blog">Blog</a></li> + <li><a href="/about">About</a></li> + + </ul> + + <a href="/" aria-label="Homepage"> + <span class="mega-octicon octicon-mark-github" title="GitHub"></span> + </a> + + <ul class="site-footer-links"> + <li>© 2014 <span title="0.04448s from github-fe129-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> + <li><a href="/site/terms">Terms</a></li> + <li><a href="/site/privacy">Privacy</a></li> + <li><a href="/security">Security</a></li> + <li><a href="/contact">Contact</a></li> + </ul> + </div><!-- /.site-footer --> +</div><!-- /.container --> + + + <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 js-suggester-field" placeholder=""></textarea> + </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-0c1b00f7935ae85624f5fc5d40d52d60febf92b4.js" type="text/javascript"></script> + <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-cbba41b870c9e4d89d40771e5c675b37b14e9601.js" type="text/javascript"></script> + + + <script async src="https://www.google-analytics.com/analytics.js"></script> + </body> +</html> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 10 23:06:15 2014 -0400 @@ -0,0 +1,727 @@ + + + + +<!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"> + + + <title>galaxytools/tool_dependencies.xml at master · bgruening/galaxytools</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="bgruening/galaxytools" name="twitter:title" /><meta content="galaxytools - Galaxy Tool wrappers" name="twitter:description" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" name="twitter:image:src" /> +<meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="https://avatars0.githubusercontent.com/u/469983?v=2&s=400" property="og:image" /><meta content="bgruening/galaxytools" property="og:title" /><meta content="https://github.com/bgruening/galaxytools" property="og:url" /><meta content="galaxytools - Galaxy Tool wrappers" property="og:description" /> + + <meta name="browser-stats-url" content="/_stats"> + <link rel="assets" href="https://assets-cdn.github.com/"> + <link rel="conduit-xhr" href="https://ghconduit.com:25035"> + <link rel="xhr-socket" href="/_sockets"> + + <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="473A4A01:7FE0:EBA77D:5411114D" name="octolytics-dimension-request_id" /><meta content="1814954" name="octolytics-actor-id" /><meta content="martenson" name="octolytics-actor-login" /><meta content="dde9ac06cabe96d1758902d5ea67b8d45f8cc402318d8a310a5cb1697f328405" name="octolytics-actor-hash" /> + <meta content="Rails, view, blob#show" name="analytics-event" /> + + + + <link rel="icon" type="image/x-icon" href="https://assets-cdn.github.com/favicon.ico"> + + + <meta content="authenticity_token" name="csrf-param" /> +<meta content="4Z9YmygaCqOF9Ke9Hiw9UJORCte4kVoQF32lw10FvRsopmD2LL8BfK5VZ9gRhaKsnnPc7sKhGEyULO4h83xElw==" name="csrf-token" /> + + <link href="https://assets-cdn.github.com/assets/github-e98a2e283e3419aa85768affc5929842870bc5fc.css" media="all" rel="stylesheet" type="text/css" /> + <link href="https://assets-cdn.github.com/assets/github2-c63e67d784fa7ee064d9610f2d22cdf8d0d7f467.css" media="all" rel="stylesheet" type="text/css" /> + + + + <meta http-equiv="x-pjax-version" content="37f365d9c8bc52a9b54820d2549e77db"> + + + <meta name="description" content="galaxytools - Galaxy Tool wrappers"> + <meta name="go-import" content="github.com/bgruening/galaxytools git https://github.com/bgruening/galaxytools.git"> + + <meta content="469983" name="octolytics-dimension-user_id" /><meta content="bgruening" name="octolytics-dimension-user_login" /><meta content="6942323" name="octolytics-dimension-repository_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="6942323" name="octolytics-dimension-repository_network_root_id" /><meta content="bgruening/galaxytools" name="octolytics-dimension-repository_network_root_nwo" /> + <link href="https://github.com/bgruening/galaxytools/commits/master.atom" rel="alternate" title="Recent Commits to galaxytools:master" type="application/atom+xml"> + + </head> + + + <body class="logged_in env-production macintosh vis-public page-blob"> + <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"> + <div class="container clearfix"> + + <a class="header-logo-invertocat" href="https://github.com/" aria-label="Homepage" ga-data-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"> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/bgruening/galaxytools/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> + <input type="text" + class="js-site-search-field is-clearable" + data-hotkey="s" + name="q" + placeholder="Search" + data-global-scope-placeholder="Search GitHub" + data-repo-scope-placeholder="Search" + tabindex="1" + autocapitalize="off"> + <div class="scope-badge">This repository</div> +</form> + </div> + <ul class="header-nav left"> + <li class="header-nav-item explore"> + <a class="header-nav-link" href="/explore" data-ga-click="Header, go to explore, text:explore">Explore</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> + <li class="header-nav-item"> + <a class="header-nav-link" href="/blog" data-ga-click="Header, go to blog, text:blog">Blog</a> + </li> + <li class="header-nav-item"> + <a class="header-nav-link" href="https://help.github.com" data-ga-click="Header, go to help, text:help">Help</a> + </li> + </ul> + + +<ul class="header-nav user-nav right" id="user-links"> + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link name" href="/martenson" data-ga-click="Header, go to profile, text:username"> + <img alt="Marten" class="avatar" data-user="1814954" height="20" src="https://avatars1.githubusercontent.com/u/1814954?v=2&s=40" width="20" /> + <span class="css-truncate"> + <span class="css-truncate-target">martenson</span> + </span> + </a> + </li> + + <li class="header-nav-item dropdown js-menu-container"> + <a class="header-nav-link js-menu-target tooltipped tooltipped-s" href="#" aria-label="Create new..." data-ga-click="Header, create new, icon:add"> + <span class="octicon octicon-plus"></span> + <span class="dropdown-caret"></span> + </a> + + <div class="dropdown-menu-content js-menu-content"> + +<ul class="dropdown-menu"> + <li> + <a href="/new"><span class="octicon octicon-repo"></span> New repository</a> + </li> + <li> + <a href="/organizations/new"><span class="octicon octicon-organization"></span> New organization</a> + </li> + + + <li class="dropdown-divider"></li> + <li class="dropdown-header"> + <span title="bgruening/galaxytools">This repository</span> + </li> + <li> + <a href="/bgruening/galaxytools/issues/new"><span class="octicon octicon-issue-opened"></span> New issue</a> + </li> +</ul> + + </div> + </li> + + <li class="header-nav-item"> + <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> + </li> + + <li class="header-nav-item"> + <a class="header-nav-link tooltipped tooltipped-s" href="/settings/profile" id="account_settings" aria-label="Settings" data-ga-click="Header, go to settings, icon:settings"> + <span class="octicon octicon-gear"></span> + </a> + </li> + + <li class="header-nav-item"> + <form accept-charset="UTF-8" action="/logout" class="logout-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="4xBMmfxsY7XX1oI5xQI2i2gzFv/xf6x15IIj2lub87XVSWTSGWpDY5PQa1qI2PlxrT4GSQElVdmRNUD9XbU2Yg==" /></div> + <button class="header-nav-link sign-out-button tooltipped tooltipped-s" aria-label="Sign out" data-ga-click="Header, sign out, icon:logout"> + <span class="octicon octicon-sign-out"></span> + </button> +</form> </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"> + +<ul class="pagehead-actions"> + + <li class="subscription"> + <form accept-charset="UTF-8" action="/notifications/subscribe" class="js-social-container" data-autosubmit="true" 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="xQc6mN1svreL+lTqg+MURSDxxWcm+llweH0/zqqMMZqQ6uq6DK84MjQxAB2/bjH0PZeZP97bDGFs/2j3sAIDZw==" /></div> <input id="repository_id" name="repository_id" type="hidden" value="6942323" /> + + <div class="select-menu js-menu-container js-select-menu"> + <a class="social-count js-social-count" href="/bgruening/galaxytools/watchers"> + 18 + </a> + <a href="/bgruening/galaxytools/subscription" + class="minibutton select-menu-button with-count js-menu-target" role="button" tabindex="0" aria-haspopup="true"> + <span class="js-select-button"> + <span class="octicon octicon-eye"></span> + Watch + </span> + </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> <!-- /.select-menu-header --> + + <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" /> + <h4>Not watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Watching</h4> + <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> <!-- /.select-menu-item --> + + <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" /> + <h4>Ignoring</h4> + <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> <!-- /.select-menu-item --> + + </div> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> + </div> <!-- /.select-menu --> + +</form> + </li> + + <li> + + <div class="js-toggler-container js-social-container starring-container on"> + + <form accept-charset="UTF-8" action="/bgruening/galaxytools/unstar" class="js-toggler-form starred js-unstar-button" 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="hX1BLjPidgGLyGX+WUaclslZi5gffSpUHUgikaubHCbcVZiOJdh9pZX7Ve4g1MrS69qyYNUqbNIvlrHyCvYHNQ==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Unstar this repository" title="Unstar bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Unstar + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> + <form accept-charset="UTF-8" action="/bgruening/galaxytools/star" class="js-toggler-form unstarred js-star-button" 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="3kLbdwpEev/anO4PVFRQa7wdfytFYEdQ0ynsR23aAMNSBJjV9NCgOBrsuU+0TCUDYd/yur7oSwV8D9yZ2p2WBA==" /></div> + <button + class="minibutton with-count js-toggler-target star-button" + aria-label="Star this repository" title="Star bgruening/galaxytools"> + <span class="octicon octicon-star"></span> + Star + </button> + <a class="social-count js-social-count" href="/bgruening/galaxytools/stargazers"> + 20 + </a> +</form> </div> + + </li> + + + <li> + <a href="/bgruening/galaxytools/fork" class="minibutton with-count js-toggler-target fork-button tooltipped-n" title="Fork your own copy of bgruening/galaxytools to your account" aria-label="Fork your own copy of bgruening/galaxytools to your account" rel="nofollow" data-method="post"> + <span class="octicon octicon-repo-forked"></span> + Fork + </a> + <a href="/bgruening/galaxytools/network" class="social-count">22</a> + </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="/bgruening" class="url fn" itemprop="url" rel="author"><span itemprop="title">bgruening</span></a></span><!-- + --><span class="path-divider">/</span><!-- + --><strong><a href="/bgruening/galaxytools" class="js-current-repository js-repo-home-link">galaxytools</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><!-- /.container --> + </div><!-- /.repohead --> + + <div class="container"> + <div class="repository-with-sidebar repo-container new-discussion-timeline "> + <div class="repository-sidebar clearfix"> + +<div class="sunken-menu vertical-right repo-nav js-repo-nav js-repository-container-pjax js-octicon-loaders" data-issue-count-url="/bgruening/galaxytools/issues/counts"> + <div class="sunken-menu-contents"> + <ul class="sunken-menu-group"> + <li class="tooltipped tooltipped-w" aria-label="Code"> + <a href="/bgruening/galaxytools" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-pjax="true" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /bgruening/galaxytools"> + <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="/bgruening/galaxytools/issues" aria-label="Issues" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /bgruening/galaxytools/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="/bgruening/galaxytools/pulls" aria-label="Pull Requests" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g p" data-selected-links="repo_pulls /bgruening/galaxytools/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="/bgruening/galaxytools/wiki" aria-label="Wiki" class="js-selected-navigation-item sunken-menu-item js-disable-pjax" data-hotkey="g w" data-selected-links="repo_wiki /bgruening/galaxytools/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="/bgruening/galaxytools/pulse/weekly" aria-label="Pulse" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="pulse /bgruening/galaxytools/pulse/weekly"> + <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="/bgruening/galaxytools/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-pjax="true" data-selected-links="repo_graphs repo_contributors /bgruening/galaxytools/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> + + + </div> +</div> + + <div class="only-with-full-nav"> + + +<div class="clone-url open" + data-protocol-type="http" + data-url="/users/set_protocol?protocol_selector=http&protocol_type=clone"> + <h3><span class="text-emphasized">HTTPS</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="ssh" + data-url="/users/set_protocol?protocol_selector=ssh&protocol_type=clone"> + <h3><span class="text-emphasized">SSH</span> clone URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="git@github.com:bgruening/galaxytools.git" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="git@github.com:bgruening/galaxytools.git" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<div class="clone-url " + data-protocol-type="subversion" + data-url="/users/set_protocol?protocol_selector=subversion&protocol_type=clone"> + <h3><span class="text-emphasized">Subversion</span> checkout URL</h3> + <div class="input-group"> + <input type="text" class="input-mini input-monospace js-url-field" + value="https://github.com/bgruening/galaxytools" readonly="readonly"> + <span class="input-group-button"> + <button aria-label="Copy to clipboard" class="js-zeroclipboard minibutton zeroclipboard-button" data-clipboard-text="https://github.com/bgruening/galaxytools" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button> + </span> + </div> +</div> + + +<p class="clone-options">You can clone with + <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a>, + <a href="#" class="js-clone-selector" data-protocol="ssh">SSH</a>, + or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>. + <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> +</p> + + <a href="http://mac.github.com" data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools" class="minibutton sidebar-button js-conduit-rewrite-url" title="Save bgruening/galaxytools to your computer and use it in GitHub Desktop." aria-label="Save bgruening/galaxytools to your computer and use it in GitHub Desktop."> + <span class="octicon octicon-device-desktop"></span> + Clone in Desktop + </a> + + + <a href="/bgruening/galaxytools/archive/master.zip" + class="minibutton sidebar-button" + aria-label="Download the contents of bgruening/galaxytools as a zip file" + title="Download the contents of bgruening/galaxytools as a zip file" + rel="nofollow"> + <span class="octicon octicon-cloud-download"></span> + Download ZIP + </a> + </div> + </div><!-- /.repository-sidebar --> + + <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container> + + +<a href="/bgruening/galaxytools/blob/3a57ada6062aa513010b1bc15048135d4207f337/samtools_sort/tool_dependencies.xml" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a> + +<!-- blob contrib key: blob_contributors:v21:cb9b2c35c78ec4af180a9b55d3c70f7a --> + +<div class="file-navigation"> + +<div class="select-menu js-menu-container js-select-menu left"> + <span class="minibutton select-menu-button js-menu-target css-truncate" data-hotkey="w" + data-master-branch="master" + data-ref="master" + title="master" + role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true"> + <span class="octicon octicon-git-branch"></span> + <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> <!-- /.select-menu-header --> + + <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" class="js-select-menu-tab">Branches</a> + </li> + <li class="select-menu-tab"> + <a href="#" data-tab-filter="tags" class="js-select-menu-tab">Tags</a> + </li> + </ul> + </div><!-- /.select-menu-tabs --> + </div><!-- /.select-menu-filters --> + + <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches"> + + <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> + + + <div class="select-menu-item js-navigation-item "> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/gh-pages/samtools_sort/tool_dependencies.xml" + data-name="gh-pages" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="gh-pages">gh-pages</a> + </div> <!-- /.select-menu-item --> + <div class="select-menu-item js-navigation-item selected"> + <span class="select-menu-item-icon octicon octicon-check"></span> + <a href="/bgruening/galaxytools/blob/master/samtools_sort/tool_dependencies.xml" + data-name="master" + data-skip-pjax="true" + rel="nofollow" + class="js-navigation-open select-menu-item-text css-truncate-target" + title="master">master</a> + </div> <!-- /.select-menu-item --> + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> <!-- /.select-menu-list --> + + <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> <!-- /.select-menu-list --> + + </div> <!-- /.select-menu-modal --> + </div> <!-- /.select-menu-modal-holder --> +</div> <!-- /.select-menu --> + + <div class="button-group right"> + <a href="/bgruening/galaxytools/find/master" + class="js-show-file-finder minibutton empty-icon tooltipped tooltipped-s" + data-pjax + data-hotkey="t" + aria-label="Quickly jump between files"> + <span class="octicon octicon-list-unordered"></span> + </a> + <button class="js-zeroclipboard minibutton zeroclipboard-button" + data-clipboard-text="samtools_sort/tool_dependencies.xml" + aria-label="Copy to clipboard" + data-copied-hint="Copied!"> + <span class="octicon octicon-clippy"></span> + </button> + </div> + + <div class="breadcrumb"> + <span class='repo-root js-repo-root'><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">galaxytools</span></a></span></span><span class="separator"> / </span><span itemscope="" itemtype="http://data-vocabulary.org/Breadcrumb"><a href="/bgruening/galaxytools/tree/master/samtools_sort" class="" data-branch="master" data-direction="back" data-pjax="true" itemscope="url"><span itemprop="title">samtools_sort</span></a></span><span class="separator"> / </span><strong class="final-path">tool_dependencies.xml</strong> + </div> +</div> + + + <div class="commit file-history-tease"> + <div class="file-history-tease-header"> + <img alt="Björn Grüning" class="avatar" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" /> + <span class="author"><a href="/bgruening" rel="author">bgruening</a></span> + <time datetime="2014-06-20T17:05:21+02:00" is="relative-time">June 20, 2014</time> + <div class="commit-title"> + <a href="/bgruening/galaxytools/commit/7e2a1f1f8338602cba2ae409df31b92bd12a97d6" class="message" data-pjax="true" title="add samtools sort">add samtools sort</a> + </div> + </div> + + <div class="participation"> + <p class="quickstat"> + <a href="#blob_contributors_box" rel="facebox"> + <strong>1</strong> + contributor + </a> + </p> + + </div> + <div id="blob_contributors_box" style="display:none"> + <h2 class="facebox-header">Users who have contributed to this file</h2> + <ul class="facebox-user-list"> + <li class="facebox-user-list-item"> + <img alt="Björn Grüning" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" /> + <a href="/bgruening">bgruening</a> + </li> + </ul> + </div> + </div> + +<div class="file-box"> + <div class="file"> + <div class="meta clearfix"> + <div class="info file-name"> + <span>7 lines (6 sloc)</span> + <span class="meta-divider"></span> + <span>0.191 kb</span> + </div> + <div class="actions"> + <div class="button-group"> + <a href="/bgruening/galaxytools/raw/master/samtools_sort/tool_dependencies.xml" class="minibutton " id="raw-url">Raw</a> + <a href="/bgruening/galaxytools/blame/master/samtools_sort/tool_dependencies.xml" class="minibutton js-update-url-with-hash">Blame</a> + <a href="/bgruening/galaxytools/commits/master/samtools_sort/tool_dependencies.xml" class="minibutton " rel="nofollow">History</a> + </div><!-- /.button-group --> + + <a class="octicon-button tooltipped tooltipped-nw js-conduit-openfile-check" + href="http://mac.github.com" + data-url="github-mac://openRepo/https://github.com/bgruening/galaxytools?branch=master&filepath=samtools_sort%2Ftool_dependencies.xml" + aria-label="Open this file in GitHub for Mac" + data-failed-title="Your version of GitHub for Mac is too old to open this file. Try checking for updates."> + <span class="octicon octicon-device-desktop"></span> + </a> + + <a class="octicon-button tooltipped tooltipped-n js-update-url-with-hash" + aria-label="Clicking this button will fork this project so you can edit the file" + href="/bgruening/galaxytools/edit/master/samtools_sort/tool_dependencies.xml" + data-method="post" rel="nofollow"><span class="octicon octicon-pencil"></span></a> + + <a class="octicon-button danger tooltipped tooltipped-s" + href="/bgruening/galaxytools/delete/master/samtools_sort/tool_dependencies.xml" + aria-label="Fork this project and delete file" + data-method="post" data-test-id="delete-blob-file" rel="nofollow"> + <span class="octicon octicon-trashcan"></span> + </a> + </div><!-- /.actions --> + </div> + + <div class="blob-wrapper data type-xml"> + <table class="highlight tab-size-8 js-file-line-container"> + <tr> + <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> + <td id="LC1" class="blob-code js-file-line"><span class="cp"><?xml version="1.0"?></span></td> + </tr> + <tr> + <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> + <td id="LC2" class="blob-code js-file-line"><span class="nt"><tool_dependency></span></td> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code js-file-line"> <span class="nt"><package</span> <span class="na">name=</span><span class="s">"samtools"</span> <span class="na">version=</span><span class="s">"0.1.19"</span><span class="nt">></span></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code js-file-line"> <span class="nt"><repository</span> <span class="na">name=</span><span class="s">"package_samtools_0_1_19"</span> <span class="na">owner=</span><span class="s">"devteam"</span> <span class="nt">/></span></td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code js-file-line"> <span class="nt"></package></span></td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code js-file-line"><span class="nt"></tool_dependency></span></td> + </tr> +</table> + + </div> + + </div> +</div> + +<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> +<div id="jump-to-line" style="display:none"> + <form accept-charset="UTF-8" class="js-jump-to-line-form"> + <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> + <button type="submit" class="button">Go</button> + </form> +</div> + + </div> + + </div><!-- /.repo-container --> + <div class="modal-backdrop"></div> + </div><!-- /.container --> + </div><!-- /.site --> + + + </div><!-- /.wrapper --> + + <div class="container"> + <div class="site-footer"> + <ul class="site-footer-links right"> + <li><a href="https://status.github.com/">Status</a></li> + <li><a href="http://developer.github.com">API</a></li> + <li><a href="http://training.github.com">Training</a></li> + <li><a href="http://shop.github.com">Shop</a></li> + <li><a href="/blog">Blog</a></li> + <li><a href="/about">About</a></li> + + </ul> + + <a href="/" aria-label="Homepage"> + <span class="mega-octicon octicon-mark-github" title="GitHub"></span> + </a> + + <ul class="site-footer-links"> + <li>© 2014 <span title="0.03477s from github-fe136-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> + <li><a href="/site/terms">Terms</a></li> + <li><a href="/site/privacy">Privacy</a></li> + <li><a href="/security">Security</a></li> + <li><a href="/contact">Contact</a></li> + </ul> + </div><!-- /.site-footer --> +</div><!-- /.container --> + + + <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 js-suggester-field" placeholder=""></textarea> + </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-0c1b00f7935ae85624f5fc5d40d52d60febf92b4.js" type="text/javascript"></script> + <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-cbba41b870c9e4d89d40771e5c675b37b14e9601.js" type="text/javascript"></script> + + + <script async src="https://www.google-analytics.com/analytics.js"></script> + </body> +</html> +