Hi Sebastian,

      I am not an expert in galaxy developing. So the following content is just 
my personal opinion. I do not think it is possible to meet you requirement. I 
reckon Galaxy searches the certain folder, defined in the universal_wsgi.ini by 
a parameter called #collect_outputs_from = new_file_path,job_working_directory. 
On top of that, a job id is required, which is the reason in the dynamic 
multiple output job id is part of the file name. If your script.py cannot 
follow the rules, Galaxy for sure cannot recognize the outputs. Normally in 
this kind of case, I write an additional script to execute the script.py with 
its original parameter and do the file manipulation afterwards. Of course this 
is not ideal, but I do nothing about python. It may be possible to write some 
complicated python code within the command tag of your wrapper file to do this. 
I am here also waiting for experts' opinions/comments.

Best regards!

On 3/21/14 9:28 AM, Sebastian Luna Valero wrote:
> 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#N
> umber_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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