All command line actions can also be ran from the web API. The API is available at https://your.server/yunohost/api. For now there's no documentation on the various routes... but you can get an idea by looking at the actionmap [here](https://github.com/YunoHost/yunohost/blob/stretch-unstable/data/actionsmap/yunohost.yml) (in particular the `api` stuff).
For example, this [PHP class](https://github.com/scith/yunohost-api-php) will allow you to administer your YunoHost instance from a PHP application (website, capacity management tool...).