I guess this is never tried prior but you may put up entry with job id in the app pending form may be with simple java code and create batch file to invoke.
You may use driver script.
Not sure on the command line option but you can trigger it via workflow.
Run Process -> Command Line -> Application-Command Reconciliation Trigger-Job
We use this to trigger a job on demand with a button on a custom form we built for doing bulk asset uploads.
Hope that helps.