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.

My problem is that I would like to see the output files in Galaxy's history without modifying the CLI interface.

To solve this problem, I have looked at the wiki page:

https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run

and the email here:

http://dev.list.galaxyproject.org/Multiple-output-files-do-not-appear-in-history-td4660470.html

However, I think that mine is a different scenario. I do not want to add new output parameters in the CLI. I would like Galaxy to bring these output files to my history without modifying the CLI options, is that possible?

Many thanks in advance for your help!

Best regards,
Sebastian.

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