First Tasks for of improvements of OpenMS and quantms

[ypriverol]

Description of feature

This issue is to control some important tasks that should be done in OpenMS core related to the current pipeline:

• Support for common enzymes (commonly found in datasets annotated in quantms) in the main search engines SAGE, COMET and MSGF+. These are the enzymes: asp-n, lys-n, arg-c, chymotrypsin, lys-c/p, lys-c, trypsin/p, glutamyl endopeptidase, trypsin, leukocyte elastase. The first iteration of this issue started here Defining more enzymes in OpenMS Comet adaptor  #354.
• Update the following tools to the latest versions: MSGF+, COMET, SAGE and Percolator.
• Extend support for all tools to accept and produce .idXML and concensusXML in compressed mode gz. This is important because the intermediate files would be good to have then compressed.

After this is implemented, we should extend quantms to support compressed files, and the new search engine versions and test with other enzymes.

[timosachsenberg]

sage is currently updated by a student:

• Updating SageAdapter with new functionality + compatibility with new Sage versions  OpenMS/OpenMS#7577
• Updating Sage Binaries OpenMS/THIRDPARTY#109

[ypriverol]

Should we then, @timosachsenberg work in MSGF+, COMET and Percolator-reset? @MaLLLiYA