I have a rather basic question about how to handle custom tools in Galaxy (I'm fresh to this framework). I am trying to link my local Galaxy with KNIME workflow that we developed in our group. I am trying to link it via a bash script that is running headless KNIME and it seems almost to work, but...

In order for this workflow to run I have to specify in the command line things like result folder or where a dynamically generated parameter file is located.

This parameter file is generate by the bash script before running KNIME. The paths will be always dynamic, depending on users etc. So I can't simply hard-code the path. Is there a way to make bash aware of where the current Galaxy user's folders and files are upon execution in Galaxy?

Below a simplified scheme of what I am doing:

User uploads txt file -> Clicks RUN -> bash script builds a parameter file (gawk ... >> param.csv) -> /knime run workflow --set the path to the parameter .csv file + set export folder

Any ideas ?

Best,

Piotr