I am configuring custom commands in Texmaker, I can use
% as a token for the name of the file (minus the extension) but I cannot find an equivalent for the full path.
I'm afraid such a token might not exist. The Texmaker manual, section 1.2 Configuring the latex related commands only mentions these tokens:
But you can see if there's a similar feature request on the Texmaker issue tracker already, and if not, file one.