I’m working on the Proteogenomics 2: Database Search tutorial and am on the Search GUI step.
The Search GUI tool (Version 4.0.41) in the usegalaxy.eu instance, seems to require an additional input: Identification Parameters file, which is missing in this tutorial. Instead there are Protein Digestion Options, Precursor options, Protein Modification Options parameters given, which I was not able to find. Is this a case of the tutorial being developed with an older version of the tool which currently has changed input files and options?
Could you please direct me as to how I could adapt the parameters in the current version of the Search GUI tool so that I can proceed with the tutorial.