In command line calling "jdownloader" is equivalent to: "java -Xmx512m -jar jdownloader.jar" (jdownloader.exe is wrapper for calling JVM with predefined parameters).
So in command line you need to build BAT/CMD file which parse the parameters and then calls specific commands or call directly JVM with available parameters.
All available parameters for command line jD:
java -jar jdownloader.jar --help
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