In MEGAN 6 UE some of the command names have changed.
Best way to find out what they are is to first do what you want to do interactively and check which commands appear in the MessageWindow as you proceed.
For example, to open the KEGG window the command is
The set command parser context command is not reported to the Message window, this is how to use it in MEGAN 6:
These two command are the same in MEGAN6:
There are some changes in the format labels for the export command in MEGAN6, again calling the desired command in GUI mode is the easiest route to finding out what the correct command is, e.g:
export what=CSV format=readName_to_keggName separator=tab counts=assigned file='/Users/huson/Desktop/test.txt';