Mercurial > repos > leqm2005 > leqm_rna_seq
changeset 0:db07b335a556 draft default tip
Uploaded
| author | leqm2005 |
|---|---|
| date | Fri, 08 Nov 2013 10:40:38 -0500 |
| parents | |
| children | |
| files | deseq_and_sam2counts |
| diffstat | 1 files changed, 404 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq_and_sam2counts Fri Nov 08 10:40:38 2013 -0500 @@ -0,0 +1,404 @@ +<!DOCTYPE HTML> + + + + + + + + + + + + + + + +<html> + <!--base_panels.mako--> + + + + <head> + <title>Galaxy Tool Shed</title> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name = "viewport" content = "maximum-scale=1.0"> + <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1"> + + <link href="/static/style/base.css?v=1383596634" media="screen" rel="Stylesheet" type="text/css" /> +<link href="/static/style/autocomplete_tagging.css?v=1383596634" media="screen" rel="Stylesheet" type="text/css" /> +<link href="/static/style/tool_menu.css?v=1383596634" media="screen" rel="Stylesheet" type="text/css" /> + + + <link href="/static/style/base.css?v=1383596634" media="screen" rel="Stylesheet" type="text/css" /> +<link href="/static/style/jquery.rating.css?v=1383596634" media="screen" rel="Stylesheet" type="text/css" /> + <style type="text/css"> + #center { + right: 0 !important; + } + </style> + + + <style type="text/css"> + body { margin: 0; padding: 0; overflow: hidden; } + #left { + background: #C1C9E5 url(/static/style/menu_bg.png) top repeat-x; + } + .unified-panel-body { + overflow: auto; + } + .toolMenu { + margin-left: 10px; + } + </style> + + + + + + + <script src="/static/scripts/libs/jquery/jquery.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/jquery/jquery.migrate.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/jquery/select2.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/bootstrap.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/underscore.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/backbone/backbone.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/backbone/backbone-relational.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/handlebars.runtime.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/galaxy.base.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/require.js?v=1383596634" type="text/javascript"></script> + + <script src="/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1383596634" type="text/javascript"></script> + + <script src="/static/scripts/mvc/ui.js?v=1383596634" type="text/javascript"></script> + + <script type="text/javascript"> + var galaxy_config = + { + root: '/' + }; + + if (window != window.top) + $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); + + // start a Galaxy namespace for objects created + window.Galaxy = window.Galaxy || {}; + + // console protection + window.console = window.console || { + log : function(){}, + debug : function(){}, + info : function(){}, + warn : function(){}, + error : function(){}, + assert : function(){} + }; + + require.config({ + baseUrl: "/static/scripts", + shim: { + "libs/underscore": { exports: "_" }, + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] + } + }); + + require(['galaxy.master', 'galaxy.frame', 'galaxy.modal', 'galaxy.upload'], function(master, frame, modal, upload) + { + Galaxy.master = new master.GalaxyMaster(); + Galaxy.frame_manager = new frame.GalaxyFrameManager(); + Galaxy.modal = new modal.GalaxyModal(); + }); + </script> + + + + </head> + + + + <body scroll="no" class="full-content "> + <div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"> + <div id="background"></div> + <div id="masthead" class="navbar navbar-fixed-top navbar-inverse"> + + + <div id="masthead" class="navbar navbar-fixed-top navbar-inverse"> + + <div style="position: relative; right: -50%; float: left;"> + <div style="display: block; position: relative; right: 50%;"> + + <ul class="nav navbar-nav" border="0" cellspacing="0"> + + + + + + <li class="" style=""> + <a class="" data-toggle="dropdown" target="_parent" href="/repository">Repositories</a> + </li> + + + + + <li class=" admin-only" style="display: none;"> + <a class="" data-toggle="dropdown" target="_parent" href="/admin">Admin</a> + </li> + + + + + <li class=" dropdown" style=""> + <a class=" dropdown-toggle" data-toggle="dropdown">Help<b class='caret'></b></a> + <ul class="dropdown-menu"> + <li> + + <a target="_blank" href="http://wiki.galaxyproject.org/Tool%20Shed">Tool Shed Wiki</a> + </li> + <li> + + <a target="_blank" href="http://wiki.g2.bx.psu.edu/Support">Support</a> + </li> + <li> + + <a target="_blank" href="http://galaxyproject.org/search/usegalaxy/">Search</a> + </li> + <li> + + <a target="_blank" href="http://wiki.galaxyproject.org/MailingLists">Mailing Lists</a> + </li> + <li> + + <a target="_blank" href="http://vimeo.com/galaxyproject">Videos</a> + </li> + <li> + + <a target="_blank" href="http://galaxyproject.org/">Wiki</a> + </li> + <li> + + <a target="_blank" href="http://wiki.galaxyproject.org/CitingGalaxy">How to Cite Galaxy</a> + </li> + </ul> + </li> + + + + + <li class=" dropdown" style=""> + <a class=" dropdown-toggle" data-toggle="dropdown">User<b class='caret'></b></a> + <ul class="dropdown-menu"> + <li> + + <a target="galaxy_main" href="/user/login">Login</a> + </li> + <li> + + <a target="galaxy_main" href="/user/create?cntrller=user">Register</a> + </li> + </ul> + </li> + + + <li class=" dropdown" style="display: none;"> + <a class=" dropdown-toggle" data-toggle="dropdown">User<b class='caret'></b></a> + <ul class="dropdown-menu"> + <li> + <a>Logged in as <span id="user-email"></span></a> + </li> + <li> + + <a target="galaxy_main" href="/user?cntrller=user">Preferences</a> + </li> + <li> + + <a target="galaxy_main" href="/user/api_keys?cntrller=user">API Keys</a> + </li> + <li> + + <a target="_top" href="/user/logout">Logout</a> + </li> + <li class="divider"></li> + </ul> + </li> + + </ul> + </div> + </div> + + <div class="navbar-brand"> + <a href="/"> + <img border="0" src="/static/images/galaxyIcon_noText.png"> + Galaxy Tool Shed + </a> + </div> + + </div> + + </div> + <div id="messagebox" class="panel-info-message"> + None + </div> + + + + + + + <div id="top-modal" class="modal fade " style='display: none;'> + <div id="top-modal-backdrop" class="modal-backdrop fade " style="z-index: -1"></div> + <div id="top-modal-dialog" class="modal-dialog"> + <div class="modal-content"> + <div class="modal-header"> + <button type='button' class='close' style="display: none;">×</button> + <h4 class='title'></h4> + </div> + <div class="modal-body"></div> + <div class="modal-footer"> + <div class="buttons" style="float: right;"></div> + <div class="extra_buttons" style=""></div> + <div style="clear: both;"></div> + </div> + </div> + </div> + </div> + + <div id="left"> + + + <div class="unified-panel-header" unselectable="on"> + <div class='unified-panel-header-inner'>3153 valid tools on Nov 04, 2013</div> + </div> + <div class="unified-panel-body"> + <div class="toolMenu"> + <div class="toolSectionList"> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + All Repositories + </div> + <div class="toolTitle"> + <a href="/repository">Browse by category</a> + </div> + </div> + </div> + </div> + + <div class="unified-panel-footer"> + <div class="panel-collapse"></span></div> + <div class="drag"></div> + </div> + </div> + <div id="center"> + + + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="/repository/view_repository?status=done&message=&id=0b029059f855f952"></iframe> + + </div> + </div> + </body> + + <script src="/static/scripts/libs/jquery/jquery.event.drag.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/jquery/jquery.event.hover.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/jquery/jquery.form.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/libs/jquery/jquery.rating.js?v=1383596634" type="text/javascript"></script> +<script src="/static/scripts/galaxy.panels.js?v=1383596634" type="text/javascript"></script> + <script type="text/javascript"> + + ensure_dd_helper(); + + var lp = new Panel( { panel: $("#left"), center: $("#center"), drag: $("#left > .unified-panel-footer > .drag" ), toggle: $("#left > .unified-panel-footer > .panel-collapse" ) } ); + force_left_panel = function( x ) { lp.force_panel( x ) }; + + + </script> + <![if !IE]> + <script type="text/javascript"> + var upload_form_error = function( msg ) { + if ( ! $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").size() ) { + $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage" name="upload_error">' + msg + '</div><p/>' ); + } else { + $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").text( msg ); + } + } + var uploads_in_progress = 0; + jQuery( function() { + $("iframe#galaxy_main").load( function() { + $(this).contents().find("form").each( function() { + if ( $(this).find("input[galaxy-ajax-upload]").length > 0 ){ + $(this).submit( function() { + // Only bother using a hidden iframe if there's a file (e.g. big data) upload + var file_upload = false; + $(this).find("input[galaxy-ajax-upload]").each( function() { + if ( $(this).val() != '' ) { + file_upload = true; + } + }); + if ( ! file_upload ) { + return true; + } + // Make a synchronous request to create the datasets first + var async_datasets; + var upload_error = false; + $.ajax( { + async: false, + type: "POST", + url: "/tool_runner/upload_async_create", + data: $(this).formSerialize(), + dataType: "json", + success: function(array_obj, status) { + if (array_obj.length > 0) { + if (array_obj[0] == 'error') { + upload_error = true; + upload_form_error(array_obj[1]); + } else { + async_datasets = array_obj.join(); + } + } else { + // ( gvk 1/22/10 ) FIXME: this block is never entered, so there may be a bug somewhere + // I've done some debugging like checking to see if array_obj is undefined, but have not + // tracked down the behavior that will result in this block being entered. I believe the + // intent was to have this block entered if the upload button is clicked on the upload + // form but no file was selected. + upload_error = true; + upload_form_error( 'No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch data.' ); + } + } + } ); + if (upload_error == true) { + return false; + } else { + $(this).find("input[name=async_datasets]").val( async_datasets ); + $(this).append("<input type='hidden' name='ajax_upload' value='true'>"); + } + // iframe submit is required for nginx (otherwise the encoding is wrong) + $(this).ajaxSubmit( { iframe: true, + complete: function (xhr, stat) { + uploads_in_progress--; + if (uploads_in_progress == 0) { + window.onbeforeunload = null; + } + } + } ); + uploads_in_progress++; + window.onbeforeunload = function() { return "Navigating away from the Galaxy analysis interface will interrupt the file upload(s) currently in progress. Do you really want to do this?"; } + if ( $(this).find("input[name='folder_id']").val() != undefined ) { + var library_id = $(this).find("input[name='library_id']").val(); + var show_deleted = $(this).find("input[name='show_deleted']").val(); + if ( location.pathname.indexOf( 'admin' ) != -1 ) { + $("iframe#galaxy_main").attr("src","/library_common/browse_library?cntrller=library_admin&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted); + } else { + $("iframe#galaxy_main").attr("src","/library_common/browse_library?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted); + } + } else { + $("iframe#galaxy_main").attr("src","/tool_runner/upload_async_message"); + } + return false; + }); + } + }); + }); + }); + </script> + <![endif]> + +</html>