IDMerger

Merges several idXML files into one idXML file.

potential predecessor tools	→ IDMerger →	potential successor tools
MascotAdapter (or other ID engines)		ConsensusID
IDFileConverter		IDMapper

The peptide hits and protein hits of the input files will be written into the single output file. In general, the number of idXML files that can be merged into one file is not limited.

If an additional file is given through the add_to parameter, identifications from the main inputs (in) are added to that file, but only for those peptide sequences that were not already present. Only the best peptide hit per identification (MS2 spectrum) is taken into account; peptide identifications and their corresponding protein identifications are transferred.

Alternatively, with the pepxml_protxml option, results from corresponding PeptideProphet and ProteinProphet runs can be combined. In this case, exactly two idXML files are expected as input: one containing data from a pepXML file, and the other containing data from a protXML file that was created based on the pepXML (meaningful results can only be obtained for matching files!). pepXML or protXML can be converted to idXML with the IDFileConverter tool.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

IDMerger -- Merges several protein/peptide identification files into one file.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDMerger.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  IDMerger <options>

Options (mandatory options marked with '*'):
  -in <files>*                      Input files separated by blanks (all must have the same type) (valid formats: 'idXML', 'oms')
  -out <file>*                      Output file (must have the same type as the input files) (valid formats: 'idXML', 'oms')
  -out_type <type>                  Output file type (default: determined from file extension) (valid: 'idXML', 'oms')
  -add_to <file>                    Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum). (valid formats: 'idXML')
  -annotate_file_origin <annotate>  Store the original filename in each protein/peptide identification (meta value: 'file_origin') - idXML input/output only (default: 'true') (valid: 'true', 'false')
  -pepxml_protxml                   Merge idXML files derived from a pepXML and corresponding protXML file.
                                    Exactly two input files are expected in this case. Not compatible with 'add_to'.
  -merge_proteins_add_PSMs          Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s. Not compatible with 'add_to'.
                                    
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

+IDMergerMerges several protein/peptide identification files into one file.

version3.4.0-pre-nightly-2024-12-16 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IDMerger'

in[] Input files separated by blanks (all must have the same type)input file*.idXML, *.oms

out Output file (must have the same type as the input files)output file*.idXML, *.oms

out_type Output file type (default: determined from file extension)idXML, oms

add_to Optional input file. IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum).input file*.idXML

annotate_file_origintrue Store the original filename in each protein/peptide identification (meta value: 'file_origin') - idXML input/output onlytrue, false

pepxml_protxmlfalse Merge idXML files derived from a pepXML and corresponding protXML file.
Exactly two input files are expected in this case. Not compatible with 'add_to'.true, false

merge_proteins_add_PSMsfalse Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s. Not compatible with 'add_to'.true, false

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 Overrides tool-specific checkstrue, false

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