To trigger a shell script or a terminal command after a transformation, you have to create a job (it’s not available in a transformation). In the following scenario I wanted to transform a HTML-File to XML using tidy.
So I define a job, where the file is created and use the step “Execute a shell script…”

then enter the tidy command:
tidy -asxhtml -numeric < file_old.html > file_new.xml
in the next tab “Script”:

Provided tidy hasn’t failed, the “file_old.html” has been converted to “file_new.xml” in your job directory.