It is possible to add JavaScript to Templates, but it must be done manually, by downloading the .tpl file, editing it using your own text editor, and then re-uploading it to the server. If you edit it using Tiki's built-in template editor, it may strip all the JavaScript from the file. In fact, with certain Templates (like header.tpl), it is recommended that you never edit the template with the Tiki editor. However, this option will not work for some items, like banners (with the "use HTML" option).
Another option is use a custom .tpl file for your banner. See here and here for more information.
Either way, you may discover that Smarty, the template language used by Tiki, doesn't like certain scripts. You may need to use the {literal} tag to avoid Smarty parsing. For more info, see the Smarty Template FAQ.
See also: Including JavaScript
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