Resolves ambiguous annotations of features with peptide identifications.

The peptide identifications are filtered so that only one identification with a single hit (with the best score) is associated to each feature. (If two IDs have the same best score, either one of them may be selected.)

Resolves ambiguous annotations of features with peptide identifications.

potential predecessor tools	$\longrightarrow$ IDConflictResolver $\longrightarrow$	potential successor tools
IDMapper		TextExporter
FeatureLinkerUnlabeled (or another feature grouping algorithm)		ProteinQuantifier

The peptide identifications are filtered so that only one identification with a single hit (with the best score) is associated to each feature. (If two IDs have the same best score, either one of them may be selected.)

The the filtered identifications are added to the vector of unassigned peptides and also reduced to a single best hit.

This step may be useful before applying ProteinQuantifier, because features with ambiguous annotation are not considered for the quantification.

The command line parameters of this tool are:

IDConflictResolver -- Resolves ambiguous annotations of features with peptide identifications
Version: 2.3.0 Apr 18 2018, 18:59:40, Revision: 2cda6bd
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  IDConflictResolver <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input file (data annotated with identifications) (valid formats: 'featureXML', 'consensu
                     sXML')
  -out <file>*       Output file (data with one peptide identification per feature) (valid formats: 'featureX
                     ML', 'consensusXML')
                     
Common TOPP options:
  -ini <file>        Use the given TOPP INI file
  -threads <n>       Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>  Writes the default configuration file
  --help             Shows options
  --helphelp         Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+IDConflictResolverResolves ambiguous annotations of features with peptide identifications

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IDConflictResolver'

in Input file (data annotated with identifications)input file*.featureXML,*.consensusXML

out Output file (data with one peptide identification per feature)output file*.featureXML,*.consensusXML

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false