Mercurial > repos > melissacline > xena_import

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xena_import	Wed Sep 03 15:29:10 2014 -0400
@@ -0,0 +1,396 @@
+<!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=1409176523" media="screen" rel="Stylesheet" type="text/css" />
+<link href="/static/style/autocomplete_tagging.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
+<link href="/static/style/tool_menu.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
+
+
+    <link href="/static/style/base.css?v=1409176523" media="screen" rel="Stylesheet" type="text/css" />
+<link href="/static/style/jquery.rating.css?v=1409176523" 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=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/jquery/jquery.migrate.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/jquery/select2.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/bootstrap.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/underscore.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/backbone/backbone.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/backbone/backbone-relational.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/handlebars.runtime.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/galaxy.base.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/require.js?v=1409176523" type="text/javascript"></script>
+
+    <script src="/static/scripts/templates/compiled/template-popupmenu-menu.js?v=1409176523" type="text/javascript"></script>
+
+    <script src="/static/scripts/mvc/ui.js?v=1409176523" type="text/javascript"></script>
+
+    <script type="text/javascript">
+        var galaxy_config = {
+            url: {
+                styles : "/static/style"
+            }
+        };
+
+        if (window != window.top)
+            $('<link href="' + galaxy_config.url.styles + '/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head');
+
+        // console protection
+        window.console = window.console || {
+            log     : function(){},
+            debug   : function(){},
+            info    : function(){},
+            warn    : function(){},
+            error   : function(){},
+            assert  : function(){}
+        };
+
+        // Set up needed paths.
+        var galaxy_paths = new GalaxyPaths({
+            root_path: '/',
+            image_path: '/static/images',
+
+            tool_url: '/api/tools',
+            history_url: '/api/histories',
+
+            datasets_url: '/api/datasets',
+            sweepster_url: '/visualization/sweepster',
+            visualization_url: '/visualization/save',
+        });
+
+        require.config({
+            baseUrl: "/static/scripts",
+            shim: {
+                "libs/underscore": { exports: "_" },
+                "libs/backbone/backbone": { exports: "Backbone" },
+                "libs/backbone/backbone-relational": ["libs/backbone/backbone"]
+            }
+        });
+
+        var frame_manager = null;
+        require(['galaxy.frame'], function(frame) { this.frame_manager = new frame.GalaxyFrameManager(galaxy_config); });
+    </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">
+                <div class="masthead-inner navbar-inner">
+
+
+    <div style="position: relative; right: -50%; float: left;">
+        <div style="display: block; position: relative; right: 50%;">
+
+            <ul class="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.g2.bx.psu.edu/Support">Support</a>
+                                        </li>
+                                        <li>
+
+                                            <a target="_blank" href="http://wiki.g2.bx.psu.edu/Tool%20Shed">Tool shed wiki</a>
+                                        </li>
+                                        <li>
+
+                                            <a target="_blank" href="http://wiki.g2.bx.psu.edu/">Galaxy wiki</a>
+                                        </li>
+                                        <li>
+
+                                            <a target="_blank" href="http://galaxycast.org">Video tutorials (screencasts)</a>
+                                        </li>
+                                        <li>
+
+                                            <a target="_blank" href="http://wiki.g2.bx.psu.edu/Citing%20Galaxy">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="title">
+        Galaxy Tool Shed
+        </a>
+    </div>
+
+                </div>
+            </div>
+            <div id="messagebox" class="panel-info-message">
+            </div>
+
+
+
+
+
+
+    <div id="overlay" style='display: none;'>
+
+        <div id="overlay-background" class="modal-backdrop fade "></div>
+
+        <div id="dialog-box" class="modal dialog-box" border="0" style='display: none;'>
+                <div class="modal-header">
+                    <span><h3 class='title'></h3></span>
+                </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 id="left">
+
+
+    <div class="unified-panel-header" unselectable="on">
+        <div class='unified-panel-header-inner'>29 valid tools on Aug 27, 2014</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=149c5ffa3420467d"></iframe>
+
+            </div>
+        </div>
+    </body>
+
+    <script src="/static/scripts/libs/jquery/jquery.event.drag.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/jquery/jquery.event.hover.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/jquery/jquery.form.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/libs/jquery/jquery.rating.js?v=1409176523" type="text/javascript"></script>
+<script src="/static/scripts/galaxy.panels.js?v=1409176523" 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>