To publish your tool using a direct link, you will use the link inside the second box on the Publish page.
Carefully select all the code inside the Direct Link box and copy it. Then paste the code into the appropriate page of your website. The link that appears will be text bearing the name of your tool. You can style the text in any manner you wish or even replace it with a button or other graphic—anything that can serve as a link to a URL. Since you are linking to a new window or tab, you are not actually pasting HTML code into your website.
This method works even if you use a template website builder like Clover and has the added benefit of bypassing the Launcher for tools that have launchers. This speeds up the time it takes for your tool to appear and frees up real estate on your website.