Hi,
Here is build command for hello_clocks_s32k144 example wiht default install paths:
./s32ds -nosplash -application org.eclipse.cdt.managedbuilder.core.headlessbuild -data ~/workspaceS32DS.ARM.2018.R1 -import ~/workspaceS32DS.ARM.2018.R1/hello_clocks_s32k144/ -cleanBuild hello_clocks_s32k144/Debug
Be sure that you are launching this command from eclipse home - by default ~/NXP/S32DS_ARM_v2018.R1/eclipse
parameters are:
-application -> eclipse managed builder
-data -> path to your S32DS workspace
-import -> path to your project
-cleanBuild -> project name including configuration (Debug in this example)

Hope it helps.
Jiri