This util provides an interface to the 'SEARCH' mode of the SpectraST program. All non-advanced parameters of the executable of SpectraST were translated into parameters of this util.

SpectraST: Version: 5

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_SpectraSTSearchAdapter.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:
  SpectraSTSearchAdapter <options>

Options (mandatory options marked with '*'):
  -executable <path>*                                                            Path to the SpectraST executable to use; may be empty if the executable is globally available.
  -spectra_files <SearchFileName1> [ <SearchFileName2> ... <SearchFileNameN> ]*  File names(s) of spectra to be searched. (valid formats: 'mzML', 'mzXML', 'mzData', 'mgf', 'dta', 'msp')
  -output_files <OutputFile1> [ <OutputFileName2> ... <OutputFileNameN> ]*       Output files. Make sure to specify one output file for each input file (valid formats: 'txt', 'tsv', 'xml', 'pepXML', 'html')
  -library_file <lib_file>.splib*                                                Specify library file. (valid formats: 'splib')
  -sequence_database_file <sequencedb_file>.fasta                                The sequence database. (valid formats: 'fasta')
  -sequence_database_type <sequencedb_type>                                      Specify type of sequence database (default: 'AA') (valid: 'DNA', 'AA')
  -search_file <search_file>                                                     Only search a subset of the query spectra in the search file (valid formats: 'txt', ' dat')
  -params_file <params_file>                                                     Read search options from file. All options set in the file will be overridden by command-line options, if specified. (valid formats: 'params')
  -precursor_mz_tolerance <precursor_mz_tolerance>                               M/z (in Th) tolerance within which candidate entries are compared to the query. Monoisotopic mass is assumed. (default: '3.0') (min: '0.0')
                                                                                 
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

+SpectraSTSearchAdapterInterface to the SEARCH Mode of the SpectraST executable

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

++1Instance '1' section for 'SpectraSTSearchAdapter'

executablespectrast Path to the SpectraST executable to use; may be empty if the executable is globally available.input file

spectra_files[] File names(s) of spectra to be searched.input file*.mzML, *.mzXML, *.mzData, *.mgf, *.dta, *.msp

output_files[] Output files. Make sure to specify one output file for each input fileoutput file*.txt, *.tsv, *.xml, *.pepXML, *.html

library_file Specify library file.input file*.splib

sequence_database_file The sequence database.input file*.fasta

sequence_database_typeAA Specify type of sequence databaseDNA, AA

search_file Only search a subset of the query spectra in the search fileinput file*.txt, *. dat

params_file Read search options from file. All options set in the file will be overridden by command-line options, if specified.input file*.params

precursor_mz_tolerance3.0 m/z (in Th) tolerance within which candidate entries are compared to the query. Monoisotopic mass is assumed.0.0:∞

use_isotopically_averaged_massfalse Use isotopically averaged mass instead of monoisotopic masstrue, false

use_all_charge_statesfalse Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrumtrue, false

user_mod_file Specify name of user-defined modifications file. Default is "spectrast.usermods".input file

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