WIP: openms 2.4

[bernt-matthias]

So far only reproduce generation of 2.3 wrappers...

TODOs:

• switch from 2.3 to 2.4
• Idea collection for the next OpenMS regenerate/merge #266
• prepare_test_data.sh uses ini files which sets parameters, either ignore it or extract parameters
• some more todos currently in generate.sh
• some tools have output flags accepting multiple files that are in 1:1 correspondence with an input flag (FileMerger.ctd MapAlignerIdentification.ctd MapAlignerIdentification.ctd MapAlignerPoseClustering.ctd MapAlignerPoseClustering.ctd MapAlignerSpectrum.ctd MapAlignerSpectrum.ctd SeedListGenerator.ctd SpecLibSearcher.ctd SpectraSTSearchAdapter.ctd)
  • create output dir
  • generate output names with a for loop over the input
  • detect outputs in a collection
• re add IDMerger logic (select_merge ...), MapAligner* logic
• read extra logic/edits in MetaproSIP MzMLSplitter SequenceCoverageCalculator postprocessing
• fixid tool id diffs (eg LowMemPeakPickerHiResRandomAccess)
• true for bool param in FeatureFinderMetabo
• remove sanitizers from selects (FeatureFinderMetabo) and data (IDMerger,MetaProSIP)
• PepNovoAdapter currently not generated (because of -models parameter). models should go to bioconda recipe or data manager needed. bioconda recipe: also fix version currently mismatch between download and version)
• proteinquantifier param_peptide_out needs proper naming to differentiate it from param_out
  Xtandem has param_xml_out -> generalize CTDConverter
• idposteriorerrorprobability outputs plot file which is a gnuplot file -> pipe through gnuplot and generate actual plot
• AssayGeneratorMetabo command not found (online docs is for call to SiriusAdapter???)
• tests
  • set format of inputs (or improve the sniffer logic of Galaxy)
• fix tool version
• add missing data types (novor, sqmass, kroenik, cachedmzml, dta, peplist, fid, dta2d, paramxml) new data types for OpenMS galaxyproject/galaxy#8109
• some tools have defaults (for files) in the ctd that are located somewhere in the env How to treat parameters with defaults in share on a linux command line OpenMS/OpenMS#4361

[bernt-matthias]

ping @bgruening just felt like starting to work on this. aim is a fully automatic script and tests. still in the beginning .. aka a good time for collecting ideas.

@jvolkening in #266 you mentioned that you could come up with a list of tools that use threads. would be helpful here.

[bgruening]

@bernt-matthias can you call me tomorrow I have a few things in mind for this.

[foellmelanie]

Hi @bernt-matthias
these are the errors I found:

• many tools: cannot find 'element_identifier' while searching for 'param_db_struct.element_identifier'
• AssayGeneratorMetabo: AssayGeneratorMetabo: command not found
• CompNovoCID: precursor_peak_tolerance = precursor_mass_tolerance in header line of idXML
• many tools: cannot find 'adv_opts'
• ExternalCalibration and InternalCalibration: Error creating a job for these tool inputs - A real number is required
• ExternalCalibration: Repeat does not make sense here
• FeatureFinderIdnetification: cannot find 'param_candidates_in'
• HighResPrecursorMassCorrector: Last test: Cannot read input file given from parameter '-feature:in'
• IDFileConverter:
  • Test4: Error: Could not determine output file type
  • Test3,6-13,15-19,22-25: Cannot read input file given from parameter '-mz_file'!
  • Test14: Allow 2 lines diff for idXML output
  • Test21: many lines differ
• FileFilter:
  • Test 1-9,11-41,43-49: ln: failed to create symbolic link 'None.data': File exists
  • Test 10: An invalid option was selected for param_spectra_remove_activation, u'Collision'
  • Test42:An invalid option was selected for param_spectra_select_polarity, u'-spectra_select_polarity'
• IDFilter:
  • Test1-19,23: ln: failed to create symbolic link 'None.data': File exists
  • Test20-22: An invalid option was selected for param_missed_cleavages_enzyme, u'Lys'
• IDMapper: Cannot read input file given from parameter '-spectra:in'!
• MetaProSIP: Conda R-version 3.3.1 and OpenMS2.4 are in conflict
• MRMTransitionGroupPicker: Parameters passed to 'MRMTransitionGroupPicker' are invalid
• MSstatsConverter: cannot find 'param_reannotate_filenames'
• OpenPepXLLF: cannot find 'param_decoy_database'
• OpenPepXL: cannot find 'param_decoy_database'
• OpenSwathConfidenceScoring: test inputfile OpenSwathConfidenceScoring_1_output.tmp is missing
• OpenSwathWorkflow: cannot find 'param_swath_windows_file'

[bernt-matthias]

superseded by #415