How do I execute MIKE Toolbox tools in batch?

You use the command ToolboxShell.exe, which is included with the MIKE installation.

Note:  all tool setups within the toolbox input file will be executed.

To execute batch jobs, you must create a text file with extension *.bat, and edit the file (right-click and select Edit):  First add the folder for the ToolboxShell executable to the overall path, then below, add one command line for each toolbox to be run, then save and execute this batch file. 

An example is given below:

start /w toolboxshell -run discharge.21t -x
start /w toolboxshell -run extract.mzt -x