I think these should be trying each AA in the list.
java -cp SearchGUI-3.2.13.jar com.compomics.cli.enzymes.EnzymesCLI -out enzymes.json -name "Elastase" -cleave_after "A,V,S,G,L,I"
Yes, you are of course correct. This code was in a beta state waiting for the new releases and therefore not really tested yet. Your changes have now been merged with the master. Thanks for the fix!
I think these should be trying each AA in the list. java -cp SearchGUI-3.2.13.jar com.compomics.cli.enzymes.EnzymesCLI -out enzymes.json -name "Elastase" -cleave_after "A,V,S,G,L,I"