Hey David, Thank you for the reply.
I will be more exhaustive in my explanation. Running the script looks something like:
% EmmaScript -t <prefix>
The program ‘EmmaScript’ needs two files of different filetypes but identical prefix (the argument passed to the program).
When I test this on my local galaxy instance I encounter this error:
ERROR: Cannot open file /home/step/galaxy/database/objects/0/f/e/dataset_0fef377a-b8fd-4029-a29d-f6cecd094a57.dat.tfam for writing
I understand this to mean that the files are not located in the environment in which the tool is executing (which I think Galaxy refers to as the job working directory?)
The two files are outputs from a previous tool and appear in my history, however I am not able to pass them as to this script (the one I am trying to wrap) since they are not exactly called as arguments- only the shared prefix is passed and the files are expected to be there.
Is it possible to make these files available in the working directory of this tool without explicitly passing them in as arguments?