OpenMS
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 29440

TICCalculator -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_TICCalculator.html
Version: 3.2.0-pre-nightly-2024-07-21 Jul 22 2024, 02:13:52, Revision: b650df0
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-pre-nightly-2024-07-21 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