| OpenMS 2.5.0

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 several peak, feature and consensus feature files. It can

- show information about the data range of a file (m/z, RT, intensity)
- show a statistical summary for intensities, qualities, feature widths
- 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:

    FileInfo -- Shows basic information about the file, such as data ranges and file type.

    Full documentation: http://www.openms.de/documentation/TOPP_FileInfo.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    Usage:

      FileInfo <options>

    Options (mandatory options marked with '*'):

      -in <file>*        Input file  (valid formats: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXM

                         L', 'consensusXML', 'idXML', 'pepXML', 'fid', 'mzid', 'trafoXML', 'fasta')

      -in_type <type>    Input file type -- default: determined from file extension or content (valid: 'mzData',

                         'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'idXML', 'pepXML',

                         'fid', 'mzid', 'trafoXML')

      -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
+FileInfo Shows basic information about the file, such as data ranges and file type.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'FileInfo'
in input file input file*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta
in_type input file type -- default: determined from file extension or content mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML
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*.csv
m false Show meta information about the whole experiment true,false
p false Shows data processing information true,false
s false Computes a five-number statistics of intensities, qualities, and widths true,false
d false Show detailed listing of all spectra and chromatograms (peak files only)true,false
c false Check for corrupt data in the file (peak files only)true,false
v false Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)true,false
i false 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)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false 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.