I am trying to implement a script into a galaxy server that I usually run on the command line.
The script produces a variable number of output files and saves those into an output directory that can be specified on the command line.
I found an article on the Galaxy wiki pages that describes this scenario: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
However, I have further questions:
What's the best way to set up the output directory? When I try to generate it from within the script, it won't let me (probably actually a good thing for security reasons...!)
Can I run a mkdir command before calling my script? If yes, do I need to specify two <command> tags in the XML tool file? One for the shell mkdir command and one for calling the perl script? (<- I tried this but couldn't get it to work)
Thanks for any ideas!