OpenMS 3.1

[bernt-matthias]

For preparation .. collecting fixes :)

• [x] truncate description to the first line: MSFragger contained a huge disclaimer :(
• [x] also GNPSExport has a long description
• [x] Fix / improve XMLValidator https://github.com/RECETOX/galaxytools/pull/319
  • [x] add xsd to galaxy datatypes https://github.com/galaxyproject/galaxy/pull/15344
  • [x] add tests from the above PR to the OpenMS code base
  • [x] update file type mapping for xsd .. xsd <-> xsd .. also xml should point to xml not bioml in gxy2oms
• [ ] try to use remote test data as much as possible
  • is it possible to rely on data from OpenMS git as much as possible?

3.1

• [ ] MapAlignerPoseClustering: out and trafo_out are not OPTIONAL_OUTPUTS .. one needs to be given.
• [ ] Sirius deprecate all/mostly or support email/password login, but OpenMS likely will drop support anyway https://github.com/OpenMS/OpenMS/issues/7000#issuecomment-1779127580
• drop adapters that require 3rd party software not available in conda
  • [ ] drop NovorAdapter (3rd party software seem not available anymore?)
  • [ ] MSFragger, MaRaClusterAdapter,MascotAdapter?
• [x] add expect_num_outputs
• [ ] Fix FLASHDecov
  • [ ] replace command section parts for -out_spec FLASHDeconv_1_spec1.csv FLASHDeconv_1_spec2.csv FLASHDeconv_1_spec3.csv (and analogously for

[bernt-matthias]

Linter errors are all: WARNING (TestsMissing): No tests found, most tools should define test cases. which won't be fixed and will be ignored for deployment.

[bernt-matthias]

Ready :)

[bgruening]

🥳🥳🎉🎉