My question is how I can modify the script to accept multiple inputs (i.e. how do I define which files in the input folder I want to be each input) and if there's a way to specify runtime parameters. For instance, the workflow I want to execute has a filter step on a tabular input item as one of the later steps which needs to be defined at runtime. How would I specify this in the 'watch_folder.py' parameters? or is this not possible yet?

For accepting multiple inputs, I'm assuming you'd differentiate your input files by a particular naming scheme, or location. Using the example_watch_folder.py as an example, you'd need to identify and upload both files (the portion creating the libset variable, you'd want to create multiple here) and finally modify the portion where the 'ds_map' is created. That dictionary is a mapping of step id's (Input Dataset steps) to the uploaded library id's from libset. As far as specifying other runtime parameters, support for this is planned but currently it isn't possible and the workflow needs to be fully predefined outside of the input datasets. Hope this helps. Thanks for using Galaxy, apologies for the delayed response, Dannon