imagemagick uses /etc/alternatives:
$ ls -l $(which convert)
lrwxrwxrwx 1 root root 25 Aug 24 2014 /usr/bin/convert -> /etc/alternatives/convert
$ ls -l /etc/alternatives/convert
lrwxrwxrwx 1 root root 20 Jul 29 2016 /etc/alternatives/convert -> /usr/bin/convert-im6
snapcraft does not process alternatives so you must create a symlink (convert -> convert-im6) yourself or make your script directly call convert-im6