Dear All,

I am trying to add a new tool in Galaxy and I have the following problem.

Let me explain a simplified example. Let's imagine that my script works from CLI as follows:

python script.py --input "input-file" --pattern "output-pattern"

After processing "input-file", the script writes several output files and their name is given according to "output-pattern".

The number of output files depends on the content of "input-file". The output files are written to the current working directory where script.py is located.

In the simplest scenario, I get only one output file in the working directory.