FileInfo

Shows basic information about the data in an OpenMS readable file.

pot. predecessor tools	→ FileInfo →	pot. successor tools
any tool operating on MS peak data (in mzML format)		none ; console or text file

This tool can show basic information about the data in different file types, such as raw peak, featureXML and consensusXML files. It can

• show information about the data range of a file (m/z, RT, ion mobility, intensity)
• show a statistical summary for intensities, qualities, feature widths, precursor charges, activation methods
• show an overview of the metadata
• validate several XML formats against their XML schema
• check for corrupt data in a file (e.g., duplicate spectra)

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

FileInfo -- Shows basic information about the file, such as data ranges and file type.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_FileInfo.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:
  FileInfo <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input file (valid formats: 'mzData', 'mzXML', 'mzML', 'sqMass', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'idXML', 'pepXML', 'mzTab', 'fid', 'mzid', 'trafoXML', 'fasta', 'pqp')
  -in_type <type>    Input file type -- default: determined from file extension or content (valid: 'mzData', 'mzXML', 'mzML', 'sqMass', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'idXML', 'pepXML', 'mzTab', 'fid', 'mzid', 'trafoXML', 'fasta', 'pqp')
  -out <file>        Optional output file. If left out, the output is written to the command line. (valid formats: 'txt')
  -m                 Show meta information about the whole experiment
  -p                 Shows data processing information
  -s                 Computes a five-number statistics of intensities, qualities, and widths
  -d                 Show detailed listing of all spectra and chromatograms (peak files only)
  -c                 Check for corrupt data in the file (peak files only)
  -v                 Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)
  -i                 Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)
                     
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

+FileInfoShows basic information about the file, such as data ranges and file type.

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

++1Instance '1' section for 'FileInfo'

in input fileinput file*.mzData, *.mzXML, *.mzML, *.sqMass, *.dta, *.dta2d, *.mgf, *.featureXML, *.consensusXML, *.idXML, *.pepXML, *.mzTab, *.fid, *.mzid, *.trafoXML, *.fasta, *.pqp

in_type input file type -- default: determined from file extension or contentmzData, mzXML, mzML, sqMass, dta, dta2d, mgf, featureXML, consensusXML, idXML, pepXML, mzTab, fid, mzid, trafoXML, fasta, pqp

out Optional output file. If left out, the output is written to the command line.output file*.txt

out_tsv Second optional output file. Tab separated flat text file.output file*.tsv

mfalse Show meta information about the whole experimenttrue, false

pfalse Shows data processing informationtrue, false

sfalse Computes a five-number statistics of intensities, qualities, and widthstrue, false

dfalse Show detailed listing of all spectra and chromatograms (peak files only)true, false

cfalse Check for corrupt data in the file (peak files only)true, false

vfalse Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)true, false

ifalse Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)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

In order to enrich the resulting data of your analysis pipeline or to quickly compare different outcomes of your pipeline you can invoke the aforementioned information of your input data and (intermediary) results.