How to set preferred domain with https in Google Webmaster Tools

Google Webmaster Tools has no option to set HTTPS as the preferred version. Google takes this automatically from your canonical link tag.

<link rel="canonical" href="https://example.com/">

So whenever the Google spider sees this line in your head section, Google automatically indexes the HTTPS version of your site.

Nowadays, Google indexes HTTPS pages by default, if it is available.

Additional Tips: If you move your site from http to https, then edit your internal webpage, and link to https version of your site. It helps to recover in drop traffic. You can use Google Webmaster Tools to find out which page is linked from which webpages.