changeset 16:5e4080791d90 draft default tip

Uploaded
author engineson
date Mon, 24 Jul 2017 08:43:45 -0400 (2017-07-24)
parents d6579f50e622
children
files readme.rst
diffstat 1 files changed, 25 insertions(+), 533 deletions(-) [+]
line wrap: on
line diff
--- a/readme.rst	Mon Jul 24 08:42:27 2017 -0400
+++ b/readme.rst	Mon Jul 24 08:43:45 2017 -0400
@@ -1,545 +1,37 @@
-
-
-
-
-
-
-<!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" href="https://assets-cdn.github.com/assets/frameworks-e04a23d39bf81b7db3c635177756ef51bc171feb440be9e174933c6eb56382da.css" media="all" rel="stylesheet" />
-  <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github-caabe7e9677dbaa4c88db92fcc52ed61b0def1a9d2e3d3ab196c0a5c81d20d04.css" media="all" rel="stylesheet" />
-  
-  
-  <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/site-4ff621027ab732d24efccdbfda10b40d3be645de22ff72aeccd01041076ef761.css" media="all" rel="stylesheet" />
-  
-
-  <meta name="viewport" content="width=device-width">
-  
-  <title>galaxy_tools/readme.rst at master · EnginesOn/galaxy_tools · GitHub</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">
-  <meta property="fb:app_id" content="1401488693436528">
-
-    
-    <meta content="https://avatars1.githubusercontent.com/u/18550486?v=3&amp;s=400" property="og:image" /><meta content="GitHub" property="og:site_name" /><meta content="object" property="og:type" /><meta content="EnginesOn/galaxy_tools" property="og:title" /><meta content="https://github.com/EnginesOn/galaxy_tools" property="og:url" /><meta content="galaxy_tools - Tool Shed repositories maintained and developed by the EnginesOn organization" property="og:description" />
-
-  <link rel="assets" href="https://assets-cdn.github.com/">
-  
-  <meta name="pjax-timeout" content="1000">
-  
-  <meta name="request-id" content="8872:424F:107FF96:1C0B105:595F77E6" 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-analytics" content="UA-3769691-2">
-
-<meta content="collector.githubapp.com" name="octolytics-host" /><meta content="github" name="octolytics-app-id" /><meta content="https://collector.githubapp.com/github-external/browser_event" name="octolytics-event-url" /><meta content="8872:424F:107FF96:1C0B105:595F77E6" name="octolytics-dimension-request_id" /><meta content="iad" name="octolytics-dimension-region_edge" /><meta content="iad" name="octolytics-dimension-region_render" />
-<meta content="/&lt;user-name&gt;/&lt;repo-name&gt;/blob/show" data-pjax-transient="true" name="analytics-location" />
-
-
-
-
-  <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="NDk4NWM3NGQ5NWRkMjc1NDdjOWYxNGM0NDQzYjQzN2RlNjY1OTE4ZDVhZmFiM2M5ZjA4MjRiOThiNDM5ZTRmZHx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI4ODcyOjQyNEY6MTA3RkY5NjoxQzBCMTA1OjU5NUY3N0U2IiwidGltZXN0YW1wIjoxNDk5NDI4ODM5LCJob3N0IjoiZ2l0aHViLmNvbSJ9">
-
+========================
+Galaxy multiqc wrapper
+========================
 
-  <meta name="html-safe-nonce" content="f994e8c4f0b29df4becc5beba1587922214b447d">
-
-  <meta http-equiv="x-pjax-version" content="f47291fda1809c6a5b3a2f5f4848063e">
-  
-
-      <link href="https://github.com/EnginesOn/galaxy_tools/commits/master.atom" rel="alternate" title="Recent Commits to galaxy_tools:master" type="application/atom+xml">
-
-  <meta name="description" content="galaxy_tools - Tool Shed repositories maintained and developed by the EnginesOn organization">
-  <meta name="go-import" content="github.com/EnginesOn/galaxy_tools git https://github.com/EnginesOn/galaxy_tools.git">
-
-  <meta content="18550486" name="octolytics-dimension-user_id" /><meta content="EnginesOn" name="octolytics-dimension-user_login" /><meta content="59100145" name="octolytics-dimension-repository_id" /><meta content="EnginesOn/galaxy_tools" name="octolytics-dimension-repository_nwo" /><meta content="true" name="octolytics-dimension-repository_public" /><meta content="false" name="octolytics-dimension-repository_is_fork" /><meta content="59100145" name="octolytics-dimension-repository_network_root_id" /><meta content="EnginesOn/galaxy_tools" name="octolytics-dimension-repository_network_root_nwo" /><meta content="false" name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" />
-
-
-    <link rel="canonical" href="https://github.com/EnginesOn/galaxy_tools/blob/master/tools/multiqc/readme.rst" 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" href="https://assets-cdn.github.com/favicon.ico">
-
-<meta name="theme-color" content="#1e2327">
-
-
-
-  </head>
-
-  <body class="logged-out env-production page-blob">
-    
-
-
+Aggregate results from bioinformatics analyses across many samples into a single report
 
-  <div class="position-relative js-header-wrapper ">
-    <a href="#start-of-content" tabindex="1" class="px-2 py-4 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="site-header js-details-container Details" role="banner">
-  <div class="site-nav-container">
-    <a class="header-logo-invertocat" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
-      <svg aria-hidden="true" class="octicon octicon-mark-github" height="32" version="1.1" viewBox="0 0 16 16" width="32"><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>
-
-    <button class="btn-link float-right site-header-toggle js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
-      <svg aria-hidden="true" class="octicon octicon-three-bars" height="24" version="1.1" viewBox="0 0 12 16" width="18"><path fill-rule="evenodd" d="M11.41 9H.59C0 9 0 8.59 0 8c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zm0-4H.59C0 5 0 4.59 0 4c0-.59 0-1 .59-1H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1h.01zM.59 11H11.4c.59 0 .59.41.59 1 0 .59 0 1-.59 1H.59C0 13 0 12.59 0 12c0-.59 0-1 .59-1z"/></svg>
-    </button>
-
-    <div class="site-header-menu">
-      <nav class="site-header-nav">
-        <a href="/features" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:features" data-selected-links="/features /features/code-review /features/project-management /features/integrations /features">
-          Features
-</a>        <a href="/business" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:business" data-selected-links="/business /business/security /business/customers /business">
-          Business
-</a>        <a href="/explore" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:explore" data-selected-links="/explore /trending /trending/developers /stars /integrations /integrations/feature/code /integrations/feature/collaborate /integrations/feature/ship showcases showcases_search showcases_landing /explore">
-          Explore
-</a>            <a href="/marketplace" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:marketplace" data-selected-links=" /marketplace">
-              Marketplace
-</a>        <a href="/pricing" class="js-selected-navigation-item nav-item" data-ga-click="Header, click, Nav menu - item:pricing" data-selected-links="/pricing /pricing/developer /pricing/team /pricing/business-hosted /pricing/business-enterprise /pricing">
-          Pricing
-</a>      </nav>
+MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
 
-      <div class="site-header-actions">
-          <div class="header-search scoped-search site-scoped-search js-site-search" role="search">
-  <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="/EnginesOn/galaxy_tools/search" class="js-site-search-form" data-scoped-search-url="/EnginesOn/galaxy_tools/search" data-unscoped-search-url="/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="&#x2713;" /></div>
-    <label class="form-control header-search-wrapper js-chromeless-input-container">
-        <a href="/EnginesOn/galaxy_tools/blob/master/tools/multiqc/readme.rst" class="header-search-scope no-underline">This repository</a>
-      <input type="text"
-        class="form-control header-search-input js-site-search-focus js-site-search-field is-clearable"
-        data-hotkey="s"
-        name="q"
-        value=""
-        placeholder="Search"
-        aria-label="Search this repository"
-        data-unscoped-placeholder="Search GitHub"
-        data-scoped-placeholder="Search"
-        autocapitalize="off">
-        <input type="hidden" class="js-site-search-type-field" name="type" >
-    </label>
-</form></div>
-
-
-          <a class="text-bold site-header-link" href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools%2Fblob%2Fmaster%2Ftools%2Fmultiqc%2Freadme.rst" 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 site-header-link" href="/join?source=header-repo" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up">Sign up</a>
-      </div>
-    </div>
-  </div>
-</header>
-
-
-  </div>
-
-  <div id="start-of-content" class="show-on-focus"></div>
-
-    <div id="js-flash-container">
-</div>
-
-
-
-  <div role="main">
-        <div itemscope itemtype="http://schema.org/SoftwareSourceCode">
-    <div id="js-repo-pjax-container" data-pjax-container>
-      
-
-
-
-  
-
-
-    <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav">
-      <div class="container repohead-details-container">
-
-        <ul class="pagehead-actions">
-  <li>
-      <a href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools"
-    class="btn btn-sm btn-with-count tooltipped tooltipped-n"
-    aria-label="You must be signed in to watch a repository" rel="nofollow">
-    <svg aria-hidden="true" class="octicon octicon-eye" height="16" version="1.1" viewBox="0 0 16 16" width="16"><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="/EnginesOn/galaxy_tools/watchers"
-     aria-label="3 users are watching this repository">
-    3
-  </a>
-
-  </li>
+============
+Installation
+============
 
-  <li>
-      <a href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools"
-    class="btn btn-sm btn-with-count tooltipped tooltipped-n"
-    aria-label="You must be signed in to star a repository" rel="nofollow">
-    <svg aria-hidden="true" class="octicon octicon-star" height="16" version="1.1" viewBox="0 0 14 16" width="14"><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-.93-4.74z"/></svg>
-    Star
-  </a>
-
-    <a class="social-count js-social-count" href="/EnginesOn/galaxy_tools/stargazers"
-      aria-label="0 users starred this repository">
-      0
-    </a>
-
-  </li>
-
-  <li>
-      <a href="/login?return_to=%2FEnginesOn%2Fgalaxy_tools"
-        class="btn btn-sm btn-with-count tooltipped tooltipped-n"
-        aria-label="You must be signed in to fork a repository" rel="nofollow">
-        <svg aria-hidden="true" class="octicon octicon-repo-forked" height="16" version="1.1" viewBox="0 0 10 16" width="10"><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="/EnginesOn/galaxy_tools/network" class="social-count"
-       aria-label="6 users forked this repository">
-      6
-    </a>
-  </li>
-</ul>
+Requirements: pkg-config
 
-        <h1 class="public ">
-  <svg aria-hidden="true" class="octicon octicon-repo" height="16" version="1.1" viewBox="0 0 12 16" width="12"><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 href="/EnginesOn" class="url fn" rel="author">EnginesOn</a></span><!--
---><span class="path-divider">/</span><!--
---><strong itemprop="name"><a href="/EnginesOn/galaxy_tools" data-pjax="#js-repo-pjax-container">galaxy_tools</a></strong>
-
-</h1>
-
-      </div>
-      <div class="container">
-        
-<nav class="reponav js-repo-nav js-sidenav-container-pjax"
-     itemscope
-     itemtype="http://schema.org/BreadcrumbList"
-     role="navigation"
-     data-pjax="#js-repo-pjax-container">
-
-  <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
-    <a href="/EnginesOn/galaxy_tools" class="js-selected-navigation-item selected reponav-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /EnginesOn/galaxy_tools" itemprop="url">
-      <svg aria-hidden="true" class="octicon octicon-code" height="16" version="1.1" viewBox="0 0 14 16" width="14"><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 href="/EnginesOn/galaxy_tools/issues" class="js-selected-navigation-item reponav-item" data-hotkey="g i" data-selected-links="repo_issues repo_labels repo_milestones /EnginesOn/galaxy_tools/issues" itemprop="url">
-        <svg aria-hidden="true" class="octicon octicon-issue-opened" height="16" version="1.1" viewBox="0 0 14 16" width="14"><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 href="/EnginesOn/galaxy_tools/pulls" class="js-selected-navigation-item reponav-item" data-hotkey="g p" data-selected-links="repo_pulls /EnginesOn/galaxy_tools/pulls" itemprop="url">
-      <svg aria-hidden="true" class="octicon octicon-git-pull-request" height="16" version="1.1" viewBox="0 0 12 16" width="12"><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>
+Conda recipe: A conda recipe exists in bioconda repository. If you have a recent Galaxy release, the packages installation is not mandatory.
 
-    <a href="/EnginesOn/galaxy_tools/projects" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /EnginesOn/galaxy_tools/projects">
-      <svg aria-hidden="true" class="octicon octicon-project" height="16" version="1.1" viewBox="0 0 15 16" width="15"><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>
-
-
-    <div class="reponav-dropdown js-menu-container">
-      <button type="button" class="btn-link reponav-item reponav-dropdown js-menu-target " data-no-toggle aria-expanded="false" aria-haspopup="true">
-        Insights
-        <svg aria-hidden="true" class="octicon octicon-triangle-down v-align-middle text-gray" height="11" version="1.1" viewBox="0 0 12 16" width="8"><path fill-rule="evenodd" d="M0 5l6 6 6-6z"/></svg>
-      </button>
-      <div class="dropdown-menu-content js-menu-content">
-        <div class="dropdown-menu dropdown-menu-sw">
-          <a class="dropdown-item" href="/EnginesOn/galaxy_tools/pulse" data-skip-pjax>
-            <svg aria-hidden="true" class="octicon octicon-pulse" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M11.5 8L8.8 5.4 6.6 8.5 5.5 1.6 2.38 8H0v2h3.6l.9-1.8.9 5.4L9 8.5l1.6 1.5H14V8z"/></svg>
-            Pulse
-          </a>
-          <a class="dropdown-item" href="/EnginesOn/galaxy_tools/graphs" data-skip-pjax>
-            <svg aria-hidden="true" class="octicon octicon-graph" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg>
-            Graphs
-          </a>
-        </div>
-      </div>
-    </div>
-</nav>
-
-      </div>
-    </div>
-
-<div class="container new-discussion-timeline experiment-repo-nav">
-  <div class="repository-content">
-
-    
-  <a href="/EnginesOn/galaxy_tools/blob/a2afe0b51bac550e9841b5116472a01ab9c7cb1b/tools/multiqc/readme.rst" class="d-none js-permalink-shortcut" data-hotkey="y">Permalink</a>
-
-  <!-- blob contrib key: blob_contributors:v21:ac5baa55b17e402dcc523a4b5ffc81e5 -->
-
-  <div class="file-navigation js-zeroclipboard-container">
-    
-<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 aria-label="Close" class="octicon octicon-x js-menu-close" height="16" role="img" version="1.1" viewBox="0 0 12 16" width="12"><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 1.48z"/></svg>
-        <span class="select-menu-title">Switch branches/tags</span>
-      </div>
+================
+Prevent displaying MultiQC webpage as gibberish
+================
 
-      <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 selected"
-               href="/EnginesOn/galaxy_tools/blob/master/tools/multiqc/readme.rst"
-               data-name="master"
-               data-skip-pjax="true"
-               rel="nofollow">
-              <svg aria-hidden="true" class="octicon octicon-check select-menu-item-icon" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M12 5l-8 8-4-4 1.5-1.5L4 10l6.5-6.5z"/></svg>
-              <span class="select-menu-item-text css-truncate-target js-select-menu-filter-text">
-                master
-              </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">
+For Galaxy to display MultiQC's HTML output properly, you need to either:
 
-
-        </div>
-
-        <div class="select-menu-no-results">Nothing to show</div>
-      </div>
-
-    </div>
-  </div>
-</div>
-
-    <div class="BtnGroup float-right">
-      <a href="/EnginesOn/galaxy_tools/find/master"
-            class="js-pjax-capture-input btn btn-sm BtnGroup-item"
-            data-pjax
-            data-hotkey="t">
-        Find file
-      </a>
-      <button aria-label="Copy file path to clipboard" class="js-zeroclipboard btn btn-sm BtnGroup-item tooltipped tooltipped-s" data-copied-hint="Copied!" type="button">Copy path</button>
-    </div>
-    <div class="breadcrumb js-zeroclipboard-target">
-      <span class="repo-root js-repo-root"><span class="js-path-segment"><a href="/EnginesOn/galaxy_tools"><span>galaxy_tools</span></a></span></span><span class="separator">/</span><span class="js-path-segment"><a href="/EnginesOn/galaxy_tools/tree/master/tools"><span>tools</span></a></span><span class="separator">/</span><span class="js-path-segment"><a href="/EnginesOn/galaxy_tools/tree/master/tools/multiqc"><span>multiqc</span></a></span><span class="separator">/</span><strong class="final-path">readme.rst</strong>
-    </div>
-  </div>
-
-
-  <include-fragment class="commit-tease" src="/EnginesOn/galaxy_tools/contributors/master/tools/multiqc/readme.rst">
-    <div>
-      Fetching contributors&hellip;
-    </div>
-
-    <div class="commit-tease-contributors">
-      <img alt="" class="loader-loading float-left" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" />
-      <span class="loader-error">Cannot retrieve contributors at this time</span>
-    </div>
-</include-fragment>
-  <div class="file">
-    <div class="file-header">
-  <div class="file-actions">
+1. Deactivate the sanitize_all_html option in galaxy.ini (sanitize_all_html = False), or
+2. Whitelist the tool in "Manage Display Whitelist" after installing
 
-    <div class="BtnGroup">
-      <a href="/EnginesOn/galaxy_tools/raw/master/tools/multiqc/readme.rst" class="btn btn-sm BtnGroup-item" id="raw-url">Raw</a>
-        <a href="/EnginesOn/galaxy_tools/blame/master/tools/multiqc/readme.rst" class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b">Blame</a>
-      <a href="/EnginesOn/galaxy_tools/commits/master/tools/multiqc/readme.rst" class="btn btn-sm BtnGroup-item" rel="nofollow">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 aria-hidden="true" class="octicon octicon-pencil" height="16" version="1.1" viewBox="0 0 14 16" width="14"><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 aria-hidden="true" class="octicon octicon-trashcan" height="16" version="1.1" viewBox="0 0 12 16" width="12"><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">
-      38 lines (25 sloc)
-      <span class="file-info-divider"></span>
-    1.03 KB
-  </div>
-</div>
-
-    
-  <div id="readme" class="readme blob instapaper_body">
-    <article class="markdown-body entry-content" itemprop="text"><a name="user-content-galaxy-multiqc-wrapper"></a>
-<h2><a id="user-content-galaxy-multiqc-wrapper" class="anchor" href="#galaxy-multiqc-wrapper" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Galaxy multiqc wrapper</h2>
-<p>Aggregate results from bioinformatics analyses across many samples into a single report</p>
-<p>MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.</p>
-<a name="user-content-installation"></a>
-<h2><a id="user-content-installation" class="anchor" href="#installation" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Installation</h2>
-<p>Requirements: pkg-config</p>
-<p>Conda recipe: A conda recipe exists in bioconda repository. If you have a recent Galaxy release, the packages installation is not mandatory.</p>
-<a name="user-content-prevent-displaying-multiqc-webpage-as-gibberish"></a>
-<h2><a id="user-content-prevent-displaying-multiqc-webpage-as-gibberish" class="anchor" href="#prevent-displaying-multiqc-webpage-as-gibberish" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Prevent displaying MultiQC webpage as gibberish</h2>
-<p>For Galaxy to display MultiQC's HTML output properly, you need to either:</p>
-<ol>
-<li>Deactivate the sanitize_all_html option in galaxy.ini (sanitize_all_html = False), or</li>
-<li>Whitelist the tool in "Manage Display Whitelist" after installing</li>
-</ol>
-<a name="user-content-history"></a>
-<h2><a id="user-content-history" class="anchor" href="#history" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>History</h2>
-<blockquote>
-<ul>
-<li>v1.0.0.0     Update to multiQC 1.0, add additional supported tools</li>
-<li>v0.6:        Initial public release</li>
-</ul>
-</blockquote>
-<a name="user-content-citation"></a>
-<h2><a id="user-content-citation" class="anchor" href="#citation" aria-hidden="true"><svg aria-hidden="true" class="octicon octicon-link" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Citation</h2>
-<p>Created by EnginesOn company</p>
-
-</article>
-  </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 accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="&#x2713;" /></div>
-      <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line&hellip;" 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>
+=======
+History
+=======
 
-    </div>
-  </div>
-
-  </div>
-
-      
-<div class="container site-footer-container">
-  <div class="site-footer " role="contentinfo">
-    <ul class="site-footer-links float-right">
-        <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact GitHub</a></li>
-      <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
-      <li><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
-      <li><a href="https://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li>
-        <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
-        <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li>
-
-    </ul>
-
-    <a href="https://github.com" aria-label="Homepage" class="site-footer-mark" title="GitHub">
-      <svg aria-hidden="true" class="octicon octicon-mark-github" height="24" version="1.1" viewBox="0 0 16 16" width="24"><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="site-footer-links">
-      <li>&copy; 2017 <span title="0.28838s from unicorn-3246185949-m426p">GitHub</span>, Inc.</li>
-        <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li>
-        <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li>
-        <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li>
-        <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
-        <li><a href="https://help.github.com" data-ga-click="Footer, go to help, text:help">Help</a></li>
-    </ul>
-  </div>
-</div>
-
-
+ * v1.0.0.0	Update to multiQC 1.0, add additional supported tools
+ * v0.6:        Initial public release
 
-  <div id="ajax-error-message" class="ajax-error-message flash flash-error">
-    <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></svg>
-    <button type="button" class="flash-close js-flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
-      <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><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 1.48z"/></svg>
-    </button>
-    You can't perform that action at this time.
-  </div>
-
+==========
+Citation
+==========
 
-    <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/compat-91f98c37fc84eac24836eec2567e9912742094369a04c4eba6e3cd1fa18902d9.js"></script>
-    <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-e2126a97ee9b5ba4bdafd0d42f4910dcb28b9f1df0ba961f8da5850dfbe403db.js"></script>
-    
-    <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-4ecb65444c34a31ac3796073302ef7c60943d4ca8ebc37ad8502df45e12fbd91.js"></script>
-    
-    
-    
-    
-  <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner d-none">
-    <svg aria-hidden="true" class="octicon octicon-alert" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.865 1.52c-.18-.31-.51-.5-.87-.5s-.69.19-.87.5L.275 13.5c-.18.31-.18.69 0 1 .19.31.52.5.87.5h13.7c.36 0 .69-.19.86-.5.17-.31.18-.69.01-1L8.865 1.52zM8.995 13h-2v-2h2v2zm0-3h-2V6h2v4z"/></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 aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><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 1.48z"/></svg>
-    </button>
-  </div>
-</div>
-
-
-  </body>
-</html>
-
+Created by EnginesOn company