Mercurial > repos > elixir-it > mutect2
changeset 1:fbfc333f3eec draft
Uploaded
author | elixir-it |
---|---|
date | Thu, 28 Jun 2018 06:07:29 -0400 |
parents | 0cc081cd3992 |
children | 1f25d6323970 |
files | mutect2_macros_add_loc.xml |
diffstat | 1 files changed, 763 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mutect2_macros_add_loc.xml Thu Jun 28 06:07:29 2018 -0400 @@ -0,0 +1,763 @@ + + + + + + +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <link rel="dns-prefetch" href="https://assets-cdn.github.com"> + <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> + <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> + <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> + <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> + <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> + <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> + + + + <link crossorigin="anonymous" media="all" integrity="sha512-pCRDtdb3GlUU48h+oRJVA8f0GddrLnU97wB7mHQ7q6c40vMbMMZsFdk0IMhkUFRqw1M/y4EkWxtaKwfeFezOkQ==" rel="stylesheet" href="https://assets-cdn.github.com/assets/frameworks-73f533b7cc08a9d040e601cfd38fa585.css" /> + <link crossorigin="anonymous" media="all" integrity="sha512-pscKt6TONS3P9zPqdDjngC5prTq2tL4UT8MfWSiqhftwRK8aipsxEuebGlIpobamrDHDV//uvSMkcPXLduUrWw==" rel="stylesheet" href="https://assets-cdn.github.com/assets/github-a0a727fb61e0eacfb1f33d2f365272f8.css" /> + + + <link crossorigin="anonymous" media="all" integrity="sha512-YBQhG++AtbZ1OJfwAkSqS9GCbbYzicxNDYKdMaLTV49eF0Lks0Bs9Egbu46uQi62AyUInQS8Cx6GGkK6uZnqFQ==" rel="stylesheet" href="https://assets-cdn.github.com/assets/site-14cf418638c848dd5bbac72b6f77dfa2.css" /> + + + <meta name="viewport" content="width=device-width"> + + <title>GDC-DNA-Seq-pipeline-galaxy-wrapper/mutect2_macros_add_loc.xml at master · pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper · GitHub</title> + <meta name="description" content="GitHub is where people build software. More than 28 million people use GitHub to discover, fork, and contribute to over 85 million projects."> + <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> + <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> + <meta property="fb:app_id" content="1401488693436528"> + + + <meta property="og:image" content="https://avatars0.githubusercontent.com/u/33326058?s=400&v=4" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta property="og:url" content="https://github.com/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta property="og:description" content="GDC-DNA-Seq-pipeline-galaxy-wrapper - galaxy wrappers GDC-DNA-Seq-pipeline" /> + + <link rel="assets" href="https://assets-cdn.github.com/"> + + <meta name="pjax-timeout" content="1000"> + + <meta name="request-id" content="B8DC:4301:BC180D:155DC99:5B34B360" data-pjax-transient> + + + + + <meta name="selected-link" value="repo_source" data-pjax-transient> + + <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU"> + <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA"> + <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc"> + <meta name="google-analytics" content="UA-3769691-2"> + +<meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="B8DC:4301:BC180D:155DC99:5B34B360" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" /> +<meta name="analytics-location" content="/<user-name>/<repo-name>/blob/show" data-pjax-transient="true" /> + + + + +<meta class="js-ga-set" name="dimension1" content="Logged Out"> + + + + + <meta name="hostname" content="github.com"> + <meta name="user-login" content=""> + + <meta name="expected-hostname" content="github.com"> + <meta name="js-proxy-site-detection-payload" content="YjU4YjQ0ZGNjMTNmZDhjMDBiZGUwNDI2NTQ2YWRiMTYxZWNiNTFlYzkwNzg4Njk0MWRjZjA5MThhNjA3MDE2NXx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiJCOERDOjQzMDE6QkMxODBEOjE1NURDOTk6NUIzNEIzNjAiLCJ0aW1lc3RhbXAiOjE1MzAxODA0NDksImhvc3QiOiJnaXRodWIuY29tIn0="> + + <meta name="enabled-features" content="UNIVERSE_BANNER,FREE_TRIALS,MARKETPLACE_INSIGHTS,MARKETPLACE_SEARCH,MARKETPLACE_INSIGHTS_CONVERSION_PERCENTAGES"> + + <meta name="html-safe-nonce" content="1eb3d9dd5c1ce4f8f0557d5d0822b0315cfeadd3"> + + <meta http-equiv="x-pjax-version" content="f3e765c121ccc4ef016361848b521709"> + + + <link href="https://github.com/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/commits/master.atom" rel="alternate" title="Recent Commits to GDC-DNA-Seq-pipeline-galaxy-wrapper:master" type="application/atom+xml"> + + <meta name="description" content="GDC-DNA-Seq-pipeline-galaxy-wrapper - galaxy wrappers GDC-DNA-Seq-pipeline"> + <meta name="go-import" content="github.com/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper git https://github.com/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper.git"> + + <meta name="octolytics-dimension-user_id" content="33326058" /><meta name="octolytics-dimension-user_login" content="pmandreoli" /><meta name="octolytics-dimension-repository_id" content="128738951" /><meta name="octolytics-dimension-repository_nwo" content="pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta name="octolytics-dimension-repository_public" content="true" /><meta name="octolytics-dimension-repository_is_fork" content="false" /><meta name="octolytics-dimension-repository_network_root_id" content="128738951" /><meta name="octolytics-dimension-repository_network_root_nwo" content="pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper" /><meta name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" content="false" /> + + + <link rel="canonical" href="https://github.com/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/Mutect2-wrapper/mutect2_macros_add_loc.xml" data-pjax-transient> + + + <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats"> + + <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors"> + + <link rel="mask-icon" href="https://assets-cdn.github.com/pinned-octocat.svg" color="#000000"> + <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://assets-cdn.github.com/favicon.ico"> + +<meta name="theme-color" content="#1e2327"> + + + +<link rel="manifest" href="/manifest.json" crossOrigin="use-credentials"> + + </head> + + <body class="logged-out env-production page-blob"> + + + <div class="position-relative js-header-wrapper "> + <a href="#start-of-content" tabindex="1" class="px-2 py-4 bg-blue text-white show-on-focus js-skip-to-content">Skip to content</a> + <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div> + + + + + + + + <header class="Header header-logged-out position-relative f4 py-3" role="banner"> + <div class="container-lg d-flex px-3"> + <div class="d-flex flex-justify-between flex-items-center"> + <a class="header-logo-invertocat my-0" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark"> + <svg height="32" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> + </a> + + </div> + + <div class="HeaderMenu HeaderMenu--bright d-flex flex-justify-between flex-auto"> + <nav class="mt-0"> + <ul class="d-flex list-style-none"> + <li class="ml-2"> + <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:features" data-selected-links="/features /features/project-management /features/code-review /features/project-management /features/integrations /features" href="/features"> + Features +</a> </li> + <li class="ml-4"> + <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:business" data-selected-links="/business /business/security /business/customers /business" href="/business"> + Business +</a> </li> + + <li class="ml-4"> + <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:explore" data-selected-links="/explore /trending /trending/developers /integrations /integrations/feature/code /integrations/feature/collaborate /integrations/feature/ship showcases showcases_search showcases_landing /explore" href="/explore"> + Explore +</a> </li> + + <li class="ml-4"> + <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:marketplace" data-selected-links=" /marketplace" href="/marketplace"> + Marketplace +</a> </li> + <li class="ml-4"> + <a class="js-selected-navigation-item HeaderNavlink px-0 py-2 m-0" data-ga-click="Header, click, Nav menu - item:pricing" data-selected-links="/pricing /pricing/developer /pricing/team /pricing/business-hosted /pricing/business-enterprise /pricing" href="/pricing"> + Pricing +</a> </li> + </ul> + </nav> + + <div class="d-flex"> + <div class="d-lg-flex flex-items-center mr-3"> + <div class="header-search scoped-search site-scoped-search js-site-search position-relative js-jump-to" + role="search combobox" + aria-owns="jump-to-results" + aria-label="Search or jump to" + aria-haspopup="listbox" + aria-expanded="true" +> + <div class="position-relative"> + <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" data-scope-type="Repository" data-scope-id="128738951" data-scoped-search-url="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/search" data-unscoped-search-url="/search" action="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> + <label class="form-control header-search-wrapper header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container"> + <input type="text" + class="form-control header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable" + data-hotkey="s,/" + name="q" + value="" + placeholder="Search" + data-unscoped-placeholder="Search GitHub" + data-scoped-placeholder="Search" + autocapitalize="off" + aria-autocomplete="list" + aria-controls="jump-to-results" + data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=s8SJYYYexWQtAM0WWDnGywuQO44UsqBgJqT1/3jB0nrix0vFhznCSWuA9kMs3tAOZ1iWtNKEvGIL8SVYe5KP9A==" + spellcheck="false" + autocomplete="off" + > + <input type="hidden" class="js-site-search-type-field" name="type" > + <img src="https://assets-cdn.github.com/images/search-shortcut-hint.svg" alt="" class="mr-2 header-search-key-slash"> + + <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container"> + <ul class="d-none js-jump-to-suggestions-template-container"> + <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item"> + <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center p-2 jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open" href=""> + <div class="jump-to-octicon js-jump-to-octicon mr-2 text-center d-none"></div> + <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar" alt="" aria-label="Team" src="" width="28" height="28"> + + <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden no-wrap css-truncate css-truncate-target"> + </div> + + <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search"> + <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> + In this repository + </span> + <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> + All GitHub + </span> + <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + + <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> + Jump to + <span class="d-inline-block ml-1 v-align-middle">↵</span> + </div> + </a> + </li> + <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-repo-octicon-template" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-project-octicon-template" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> + <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-search-octicon-template" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg> + </ul> + <ul class="d-none js-jump-to-no-results-template-container"> + <li class="d-flex flex-justify-center flex-items-center p-3 f5 d-none"> + <span class="text-gray">No suggested jump to results</span> + </li> + </ul> + + <ul id="jump-to-results" class="js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container" > + <li class="d-flex flex-justify-center flex-items-center p-0 f5"> + <img src="https://assets-cdn.github.com/images/spinners/octocat-spinner-128.gif" alt="Octocat Spinner Icon" class="m-2" width="28"> + </li> + </ul> + </div> + </label> +</form> </div> +</div> + + </div> + + <span class="d-inline-block"> + <div class="HeaderNavlink px-0 py-2 m-0"> + <a class="text-bold text-white no-underline" href="/login?return_to=%2Fpmandreoli%2FGDC-DNA-Seq-pipeline-galaxy-wrapper%2Fblob%2Fmaster%2FMutect2-wrapper%2Fmutect2_macros_add_loc.xml" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in">Sign in</a> + <span class="text-gray">or</span> + <a class="text-bold text-white no-underline" href="/join?source=header-repo" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a> + </div> + </span> + </div> + </div> + </div> +</header> + + </div> + + <div id="start-of-content" class="show-on-focus"></div> + + <div id="js-flash-container"> +</div> + + + + <div role="main" class="application-main "> + <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> + <div id="js-repo-pjax-container" data-pjax-container > + + + + + + + + + <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav "> + <div class="repohead-details-container clearfix container"> + + <ul class="pagehead-actions"> + <li> + <a href="/login?return_to=%2Fpmandreoli%2FGDC-DNA-Seq-pipeline-galaxy-wrapper" + class="btn btn-sm btn-with-count tooltipped tooltipped-n" + aria-label="You must be signed in to watch a repository" rel="nofollow"> + <svg class="octicon octicon-eye" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg> + Watch + </a> + <a class="social-count" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/watchers" + aria-label="0 users are watching this repository"> + 0 + </a> + + </li> + + <li> + <a href="/login?return_to=%2Fpmandreoli%2FGDC-DNA-Seq-pipeline-galaxy-wrapper" + class="btn btn-sm btn-with-count tooltipped tooltipped-n" + aria-label="You must be signed in to star a repository" rel="nofollow"> + <svg class="octicon octicon-star" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74L14 6z"/></svg> + Star + </a> + + <a class="social-count js-social-count" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/stargazers" + aria-label="0 users starred this repository"> + 0 + </a> + + </li> + + <li> + <a href="/login?return_to=%2Fpmandreoli%2FGDC-DNA-Seq-pipeline-galaxy-wrapper" + class="btn btn-sm btn-with-count tooltipped tooltipped-n" + aria-label="You must be signed in to fork a repository" rel="nofollow"> + <svg class="octicon octicon-repo-forked" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> + Fork + </a> + + <a href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/network" class="social-count" + aria-label="1 user forked this repository"> + 1 + </a> + </li> +</ul> + + <h1 class="public "> + <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg> + <span class="author" itemprop="author"><a class="url fn" rel="author" href="/pmandreoli">pmandreoli</a></span><!-- +--><span class="path-divider">/</span><!-- +--><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper">GDC-DNA-Seq-pipeline-galaxy-wrapper</a></strong> + +</h1> + + </div> + +<nav class="reponav js-repo-nav js-sidenav-container-pjax container" + itemscope + itemtype="http://schema.org/BreadcrumbList" + role="navigation" + data-pjax="#js-repo-pjax-container"> + + <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> + <a class="js-selected-navigation-item selected reponav-item" itemprop="url" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper"> + <svg class="octicon octicon-code" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg> + <span itemprop="name">Code</span> + <meta itemprop="position" content="1"> +</a> </span> + + <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> + <a itemprop="url" data-hotkey="g i" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/issues" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/issues"> + <svg class="octicon octicon-issue-opened" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"/></svg> + <span itemprop="name">Issues</span> + <span class="Counter">0</span> + <meta itemprop="position" content="2"> +</a> </span> + + <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement"> + <a data-hotkey="g p" itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulls" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulls"> + <svg class="octicon octicon-git-pull-request" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg> + <span itemprop="name">Pull requests</span> + <span class="Counter">0</span> + <meta itemprop="position" content="3"> +</a> </span> + + <a data-hotkey="g b" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/projects" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/projects"> + <svg class="octicon octicon-project" viewBox="0 0 15 16" version="1.1" width="15" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg> + Projects + <span class="Counter" >0</span> +</a> + + + <a class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors dependency_graph pulse /pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulse" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/pulse"> + <svg class="octicon octicon-graph" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg> + Insights +</a> + +</nav> + + + </div> + +<div class="container new-discussion-timeline experiment-repo-nav "> + <div class="repository-content "> + + + <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/bf2daac4de1923ee01fd86ad0683e1ef5a9bd82e/Mutect2-wrapper/mutect2_macros_add_loc.xml">Permalink</a> + + <!-- blob contrib key: blob_contributors:v21:b9a2173360ae3ea06528ce8f26184de1 --> + + <div class="signup-prompt-bg rounded-1"> + <div class="signup-prompt p-4 text-center mb-4 rounded-1"> + <div class="position-relative"> + <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/site/dismiss_signup_prompt" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="✓" /><input type="hidden" name="authenticity_token" value="2q5EdBepxNgbE/Yv2lKtLU5OtZ0KL+K2ARE8s26fvpW0wDB9wrolkXjlDD9+iZmhPoCu2EVhU8NdcLYDaW3Sig==" /> + <button type="submit" class="position-absolute top-0 right-0 btn-link link-gray" data-ga-click="(Logged out) Sign up prompt, clicked Dismiss, text:dismiss"> + Dismiss + </button> +</form> <h3 class="pt-2">Join GitHub today</h3> + <p class="col-6 mx-auto">GitHub is home to over 28 million developers working together to host and review code, manage projects, and build software together.</p> + <a class="btn btn-primary" href="/join?source=prompt-blob-show" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up">Sign up</a> + </div> + </div> + </div> + + + <div class="file-navigation"> + +<div class="select-menu branch-select-menu js-menu-container js-select-menu float-left"> + <button class=" btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w" + + type="button" aria-label="Switch branches or tags" aria-expanded="false" aria-haspopup="true"> + <i>Branch:</i> + <span class="js-select-button css-truncate-target">master</span> + </button> + + <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax> + + <div class="select-menu-modal"> + <div class="select-menu-header"> + <svg class="octicon octicon-x js-menu-close" role="img" aria-label="Close" viewBox="0 0 12 16" version="1.1" width="12" height="16"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> + <span class="select-menu-title">Switch branches/tags</span> + </div> + + <div class="select-menu-filters"> + <div class="select-menu-text-filter"> + <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="form-control js-filterable-field js-navigation-enable" placeholder="Filter branches/tags"> + </div> + <div class="select-menu-tabs"> + <ul> + <li class="select-menu-tab"> + <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab" role="tab">Branches</a> + </li> + <li class="select-menu-tab"> + <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab" role="tab">Tags</a> + </li> + </ul> + </div> + </div> + + <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches" role="menu"> + + <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> + + + <a class="select-menu-item js-navigation-item js-navigation-open " + href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/dev/Mutect2-wrapper/mutect2_macros_add_loc.xml" + data-name="dev" + data-skip-pjax="true" + rel="nofollow"> + <svg class="octicon octicon-check select-menu-item-icon" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5L12 5z"/></svg> + <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text"> + dev + </span> + </a> + <a class="select-menu-item js-navigation-item js-navigation-open selected" + href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/master/Mutect2-wrapper/mutect2_macros_add_loc.xml" + data-name="master" + data-skip-pjax="true" + rel="nofollow"> + <svg class="octicon octicon-check select-menu-item-icon" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5L12 5z"/></svg> + <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text"> + master + </span> + </a> + <a class="select-menu-item js-navigation-item js-navigation-open " + href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blob/test/Mutect2-wrapper/mutect2_macros_add_loc.xml" + data-name="test" + data-skip-pjax="true" + rel="nofollow"> + <svg class="octicon octicon-check select-menu-item-icon" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5L12 5z"/></svg> + <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text"> + test + </span> + </a> + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> + + <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags"> + <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> + + + </div> + + <div class="select-menu-no-results">Nothing to show</div> + </div> + + </div> + </div> +</div> + + <div class="BtnGroup float-right"> + <a href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/find/master" + class="js-pjax-capture-input btn btn-sm BtnGroup-item" + data-pjax + data-hotkey="t"> + Find file + </a> + <clipboard-copy for="blob-path" class="btn btn-sm BtnGroup-item"> + Copy path + </clipboard-copy> + </div> + <div id="blob-path" class="breadcrumb"> + <span class="repo-root js-repo-root"><span class="js-path-segment"><a data-pjax="true" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper"><span>GDC-DNA-Seq-pipeline-galaxy-wrapper</span></a></span></span><span class="separator">/</span><span class="js-path-segment"><a data-pjax="true" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/tree/master/Mutect2-wrapper"><span>Mutect2-wrapper</span></a></span><span class="separator">/</span><strong class="final-path">mutect2_macros_add_loc.xml</strong> + </div> + </div> + + + + <div class="commit-tease"> + <span class="float-right"> + <a class="commit-tease-sha" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/163a49b5746b79e0245049afc0fcfb8ca220e494" data-pjax> + 163a49b + </a> + <relative-time datetime="2018-06-27T09:23:15Z">Jun 27, 2018</relative-time> + </span> + <div> + <a rel="author" data-skip-pjax="true" data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli"><img class="avatar" src="https://avatars0.githubusercontent.com/u/33326058?s=40&v=4" width="20" height="20" alt="@pmandreoli" /></a> + <a class="user-mention" rel="author" data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli">pmandreoli</a> + <a data-pjax="true" title="change" class="message" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/commit/163a49b5746b79e0245049afc0fcfb8ca220e494">change</a> + </div> + + <div class="commit-tease-contributors"> + <button type="button" class="btn-link muted-link contributors-toggle" data-facebox="#blob_contributors_box"> + <strong>1</strong> + contributor + </button> + + </div> + + <div id="blob_contributors_box" style="display:none"> + <h2 class="facebox-header" data-facebox-id="facebox-header">Users who have contributed to this file</h2> + <ul class="facebox-user-list" data-facebox-id="facebox-description"> + <li class="facebox-user-list-item"> + <a class="d-inline-block" data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli"><img src="https://avatars1.githubusercontent.com/u/33326058?s=48&v=4" width="24" height="24" alt="@pmandreoli" /></a> + <a data-hovercard-user-id="33326058" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/pmandreoli">pmandreoli</a> + </li> + </ul> + </div> + </div> + + + + <div class="file"> + <div class="file-header"> + <div class="file-actions"> + + <div class="BtnGroup"> + <a id="raw-url" class="btn btn-sm BtnGroup-item" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/raw/master/Mutect2-wrapper/mutect2_macros_add_loc.xml">Raw</a> + <a class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blame/master/Mutect2-wrapper/mutect2_macros_add_loc.xml">Blame</a> + <a rel="nofollow" class="btn btn-sm BtnGroup-item" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/commits/master/Mutect2-wrapper/mutect2_macros_add_loc.xml">History</a> + </div> + + + <button type="button" class="btn-octicon disabled tooltipped tooltipped-nw" + aria-label="You must be signed in to make or propose changes"> + <svg class="octicon octicon-pencil" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg> + </button> + <button type="button" class="btn-octicon btn-octicon-danger disabled tooltipped tooltipped-nw" + aria-label="You must be signed in to make or propose changes"> + <svg class="octicon octicon-trashcan" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg> + </button> + </div> + + <div class="file-info"> + 23 lines (22 sloc) + <span class="file-info-divider"></span> + 1.39 KB + </div> +</div> + + + + <div itemprop="text" class="blob-wrapper data type-xml"> + <table class="highlight tab-size js-file-line-container" data-tab-size="8"> + <tr> + <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> + <td id="LC1" class="blob-code blob-code-inner js-file-line"><<span class="pl-ent">macros</span>></td> + </tr> + <tr> + <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> + <td id="LC2" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">macro</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reference_loc<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">conditional</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reference_source<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>reference_source_selector<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Will you select a reference genome from your history or use a built-in index?<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Built-ins were indexed using default options. See `Indexes` section of help below<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cached<span class="pl-pds">"</span></span>>Use a built-in genome index</<span class="pl-ent">option</span>></td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>history<span class="pl-pds">"</span></span>>Use a genome from history and build index</<span class="pl-ent">option</span>></td> + </tr> + <tr> + <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> + <td id="LC7" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> + <td id="LC8" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>cached<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> + <td id="LC9" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>ref_file<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Using reference genome<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>Select genome from the list<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> + <td id="LC10" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">options</span> <span class="pl-e">from_data_table</span>=<span class="pl-s"><span class="pl-pds">"</span>mutect2_indexes<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> + <td id="LC11" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">filter</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>sort_by<span class="pl-pds">"</span></span> <span class="pl-e">column</span>=<span class="pl-s"><span class="pl-pds">"</span>2<span class="pl-pds">"</span></span> /></td> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">validator</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>no_options<span class="pl-pds">"</span></span> <span class="pl-e">message</span>=<span class="pl-s"><span class="pl-pds">"</span>No indexes are available<span class="pl-pds">"</span></span> /></td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">options</span>></td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">validator</span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>no_options<span class="pl-pds">"</span></span> <span class="pl-e">message</span>=<span class="pl-s"><span class="pl-pds">"</span>A built-in reference genome is not available for the build associated with the selected input file<span class="pl-pds">"</span></span>/></td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s"><span class="pl-pds">"</span>history<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code blob-code-inner js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s"><span class="pl-pds">"</span>ref_file<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s"><span class="pl-pds">"</span>data<span class="pl-pds">"</span></span> <span class="pl-e">format</span>=<span class="pl-s"><span class="pl-pds">"</span>fasta<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s"><span class="pl-pds">"</span>Use the following dataset as the reference sequence<span class="pl-pds">"</span></span> <span class="pl-e">help</span>=<span class="pl-s"><span class="pl-pds">"</span>You can upload a FASTA sequence to the history and use it as reference<span class="pl-pds">"</span></span> /></td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">when</span>> </td> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code blob-code-inner js-file-line"> </<span class="pl-ent">macro</span>></td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code blob-code-inner js-file-line"></<span class="pl-ent">macros</span>></td> + </tr> +</table> + + <div class="BlobToolbar position-absolute js-file-line-actions dropdown js-menu-container js-select-menu d-none" aria-hidden="true"> + <button class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1 js-menu-target" type="button" aria-expanded="false" aria-haspopup="true" aria-label="Inline file action toolbar" aria-controls="inline-file-actions"> + <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg> + </button> + <div class="dropdown-menu-content js-menu-content" id="inline-file-actions"> + <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2"> + <li><clipboard-copy class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li> + <li><clipboard-copy class="dropdown-item" id="js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</clipboard-copy></li> + <li><a class="dropdown-item js-update-url-with-hash" id="js-view-git-blame" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/blame/bf2daac4de1923ee01fd86ad0683e1ef5a9bd82e/Mutect2-wrapper/mutect2_macros_add_loc.xml">View git blame</a></li> + <li><a class="dropdown-item" id="js-new-issue" href="/pmandreoli/GDC-DNA-Seq-pipeline-galaxy-wrapper/issues/new">Open new issue</a></li> + </ul> + </div> + </div> + + </div> + + </div> + + <button type="button" data-facebox="#jump-to-line" data-facebox-class="linejump" data-hotkey="l" class="d-none">Jump to Line</button> + <div id="jump-to-line" style="display:none"> + <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form" action="" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="✓" /> + <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus> + <button type="submit" class="btn">Go</button> +</form> </div> + + + </div> + <div class="modal-backdrop js-touch-events"></div> +</div> + + </div> + </div> + + </div> + + +<div class="footer container-lg px-3" role="contentinfo"> + <div class="position-relative d-flex flex-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light "> + <ul class="list-style-none d-flex flex-wrap "> + <li class="mr-3">© 2018 <span title="0.24046s from unicorn-4147889289-kxlp9">GitHub</span>, Inc.</li> + <li class="mr-3"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li> + <li class="mr-3"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li> + <li class="mr-3"><a href="https://help.github.com/articles/github-security/" data-ga-click="Footer, go to security, text:security">Security</a></li> + <li class="mr-3"><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> + <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li> + </ul> + + <a aria-label="Homepage" title="GitHub" class="footer-octicon" href="https://github.com"> + <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg> +</a> + <ul class="list-style-none d-flex flex-wrap "> + <li class="mr-3"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li> + <li class="mr-3"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> + <li class="mr-3"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> + <li class="mr-3"><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> + <li class="mr-3"><a href="https://blog.github.com" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> + <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li> + + </ul> + </div> + <div class="d-flex flex-justify-center pb-6"> + <span class="f6 text-gray-light"></span> + </div> +</div> + + + + <div id="ajax-error-message" class="ajax-error-message flash flash-error"> + <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg> + <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> + <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> + </button> + You can’t perform that action at this time. + </div> + + + <script crossorigin="anonymous" integrity="sha512-wIuAKDhvxe9wCaNR1tzCk3rtl+wXEWC28rmRpzmx0h98VEeWC6Y3xCWV1xAW6NP6eQQX+x8ZGhW6Sdut+mLRuw==" type="application/javascript" src="https://assets-cdn.github.com/assets/compat-a48960bafc17c30572990bbab3664e9c.js"></script> + <script crossorigin="anonymous" integrity="sha512-rQ5rqxNcZevFDDt0YpFyUsMdf6ORyN1evQjIGwQGbiIaLrROmN77NgRxz+EOtW1VEo75v97gppFprSCKLq0s9w==" type="application/javascript" src="https://assets-cdn.github.com/assets/frameworks-6ad64ae8a533d7550b0f4b5b12d08ee7.js"></script> + + <script crossorigin="anonymous" async="async" integrity="sha512-MluPTi4ElJIVCIU3rFJ7lVukR7SJi6Bhws96FO91NpNHbE7Mnf5ymDBf6e+xJKQr4xzw/5XrjvrNmdnVGNSagg==" type="application/javascript" src="https://assets-cdn.github.com/assets/github-9e1fb62f0965afe7d5d91ca5b5c1e71d.js"></script> + + + + <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner d-none"> + <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg> + <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> + <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> + </div> + <div class="facebox" id="facebox" style="display:none;"> + <div class="facebox-popup"> + <div class="facebox-content" role="dialog" aria-labelledby="facebox-header" aria-describedby="facebox-description"> + </div> + <button type="button" class="facebox-close js-facebox-close" aria-label="Close modal"> + <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg> + </button> + </div> +</div> + + <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0"> + <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;"> + </div> +</div> + +<div id="hovercard-aria-description" class="sr-only"> + Press h to open a hovercard with more details. +</div> + + + </body> +</html> +