Hi all! I'm working with a large number of files, and each file has the sample's expansion factor in the title. One tool I use part-way through my analysis requires that expansion factor to be entered as a parameter. Instead I'd like to be able to run these files in a pipeline in batch with the expansion factor automatically taken from the name of each file, but I can't find a way to do that. If I were working with python I could use the split function since everything is named uniformly and the expansion factor is the 4th segment when splitting by "_". However, I don't think even using a similar function in the xml file (if such a function exists for the command line) would work, because the actual name of the file would be something like 3212.dat due to galaxy's internal naming rules.
Basically I'm looking for a way to use part of the title of a file as a flag / parameter in my xml file, if there is a way. Running the fitness calculation tool on each individual file by hand and entering the expansion factor myself each time takes a long time and it's quite dull. If anyone has any ideas I'd appreciate them!