IDRipper

IDRipper splits the protein/peptide identifications of an idXML file into several idXML files according their annotated file origin.

potential predecessor tools	→ IDRipper→	potential successor tools
IDFilter		IDMapper

Example

Assuming each peptide identification in a given idXML file is annotated with its file origin (e.g. IDRipper_test.idXML) :

<userParam type="string" name="file_origin" value="IDMerger1_test.idXML"/> or
<userParam type="string" name="file_origin" value="IDMerger2_test.idXML"/>

Obviously the file contains protein/peptide identifications of IDMerger1_test.idXML and IDMerger2_test.idXML.

Calling IDRipper with an input file (here: -in IDRipper_test.idXML) and an output directory (via out) will result in two idXML files stored in the specified directory and named according to their file origin.

In theory, merging files with IDMerger and splitting the resulting file with IDRipper will result in the original input files.

NOTE: The meta value "file_origin" is removed by the IDSplitter!

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

IDRipper -- Split protein/peptide identification file into several files according to identification run and annotated file origin.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_IDRipper.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:
  IDRipper <options>

Options (mandatory options marked with '*'):
  -in <file>*          Input file, in which the protein/peptide identifications must be tagged with 'file_origin' (valid formats: 'idXML')
  -out <directory>*    Path to the output directory to write the ripped files to.
  -numeric_filenames   Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes.
  -split_ident_runs    Split different identification runs into separate files.
                       
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

+IDRipperSplit protein/peptide identification file into several files according to identification run and annotated file origin.

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

++1Instance '1' section for 'IDRipper'

in Input file, in which the protein/peptide identifications must be tagged with 'file_origin'input file*.idXML

out Path to the output directory to write the ripped files to.output prefix

numeric_filenamesfalse Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes.true, false

split_ident_runsfalse Split different identification runs into separate files.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