I would like to be able to go to a webpage select a few options and then run a command line script with those options. Is this possible with qooxdoo?
Of course, but you will need a few additional pieces. You can create the web page with qooxdoo, e.g. using qooxdoo's form elements (qx.ui.form.*). You then need a backend you can submit the form data to (any old Apache will do, as will a Node.js server). In the backend you will need some custom code to create a subshell and run the command on it (e.g. with PHP, mod_perl, mod_wsgi, ..., JS), adding in the options from the web form.