what you want is currently not possible from within HeuristicLab. The only command line arguments that are supported are starting an applications from Heuristiclab, such as the Optimizer.
However, you could write your own C# program that performs that actions you need and which uses HeuristicLab just as a library instead of a program. Therefore, you need to load all necessary plugins manually and then perform your actions. The same use case is implemented in the unit tests of HeuristicLab where algorithms are loaded from a file and executed.
For example the GeneticAlgorithmTest  loads a GA from a file, executes the algorithm and compares the results with the expected ones. A prerequisite is that all necessary plugins are loaded and this functionality is provided by the PluginLoader class.
I hope this helps and you can programmatically use HeuristicLab.
All the best,
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