| OpenMS 2.5.0

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:

    IDMerger -- Merges several protein/peptide identification files into one file.

    Full documentation: http://www.openms.de/documentation/TOPP_IDMerger.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

      IDMerger <options>

    Options (mandatory options marked with '*'):

      -in <files>*               Input files separated by blanks (valid formats: 'idXML')

      -out <file>*               Output file (valid formats: 'idXML')

      -add_to <file>             Optional input file. IDs from 'in' are added to this file, but only if the (modi

                                 fied) peptide sequences are not present yet (considering only best hits per spec

                                 trum). (valid formats: 'idXML')

      -annotate_file_origin      Store the original filename in each protein/peptide identification (meta value:

                                 file_origin).

      -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 comp

                                 atible 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
+IDMerger Merges several protein/peptide identification files into one file.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'IDMerger'
in[] Input files separated by blanks input file*.idXML
out Output file output file*.idXML
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_origin false Store the original filename in each protein/peptide identification (meta value: file_origin).true,false
pepxml_protxml false 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_PSMs false 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)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false