Designer Automation API
With this API, you can create WorkflowXMLs programmatically.
IWR works with default license installed to a physical computer or on Central Licensing Server (No OEM).

IWR.exe is basically a development tool but you can easily implement your own version of it. Its source is located in OmniPage\CSDK21\Samples\WorkflowRunner\IWR folder.
If you have multiple input files for a workflow, you can also specify them, therefore /i:inputA.tif,inputB.tif means replacing this:
<Inputs type="array">
<Input type="string" value="$inputfile1$" />
</Inputs>
With this:
<Inputs type="array">
<Input type="string" value="inputA.tif" />
<Input type="string" value="inputB.tif" />
</Inputs>