You can indeed to do it with the Input Transformer.
In module 1 set the notes (value 1:equal:<note name/number>) that need to be transposed in the Filter pane.
Set their transpositions in the Action pane. (Value 1:Subtract:)
Be sure to set all the booleans on the right to OR. Then activate the module.
In module 2 filter target is equal:note, action target is Value 1:subtract (or add) what you need to get the transposition you need. This transposes the all the pitches together.
Let’s say you want to set up a harmonic minor scale. Put the notes needing transposition in the Filter pane, and put the value by which they will be transposed in the action pane.
See example.
