TICCalculator

Calculates the TIC of a raw mass spectrometric file.

This class was developed to benchmark multiple methods inside OpenMS for reading raw mass spectrometric data. It can be used for benchmarking these different methods as well as benchmarking external tools. Of course you can also calculate the TIC with this tool.

The command line parameters of this tool are:

 Memory consumption before 29696

TICCalculator -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
Full documentation: http://www.openms.de/doxygen/release/3.2.0/html/TOPP_TICCalculator.html
Version: 3.2.0 Sep 18 2024, 16:00:56, Revision: e231942
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  TICCalculator <options>

Options (mandatory options marked with '*'):
  -in <file>*            Input file to convert. (valid formats: 'mzData', 'mzXML', 'mzML', 'cachedMzML', 'dta
                         ', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'ms2', 'fid', 'tsv', 'peplist', 
                         'kroenik', 'edta')
  -in_type <type>        Input file type -- default: determined from file extension or content
                          (valid: 'mzData', 'mzXML', 'mzML', 'cachedMzML', 'dta', 'dta2d', 'mgf', 'featureXML
                         ', 'consensusXML', 'ms2', 'fid', 'tsv', 'peplist', 'kroenik', 'edta')
  -read_method <method>  Method to read the file (default: 'regular') (valid: 'regular', 'indexed', 'indexed_
                         parallel', 'streaming', 'cached', 'cached_parallel')
  -loadData <method>     Whether to actually load and decode the binary data (or whether to skip decoding 
                         the binary data) (default: 'true') (valid: 'true', 'false')
                         
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)

 Memory consumption final 30848

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+TICCalculatorCalculates the TIC from a mass spectrometric raw file (useful for benchmarking).

version3.2.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'TICCalculator'

in Input file to convert.input file*.mzData, *.mzXML, *.mzML, *.cachedMzML, *.dta, *.dta2d, *.mgf, *.featureXML, *.consensusXML, *.ms2, *.fid, *.tsv, *.peplist, *.kroenik, *.edta

in_type Input file type -- default: determined from file extension or content
mzData, mzXML, mzML, cachedMzML, dta, dta2d, mgf, featureXML, consensusXML, ms2, fid, tsv, peplist, kroenik, edta

read_methodregular Method to read the fileregular, indexed, indexed_parallel, streaming, cached, cached_parallel

loadDatatrue Whether to actually load and decode the binary data (or whether to skip decoding the binary data)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