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FileConverter

Converts between different MS file formats.

pot. predecessor tools $ \longrightarrow $ FileConverter $ \longrightarrow $ pot. successor tools
GenericWrapper (e.g. for calling external converters) any tool operating on the output format
any vendor software exporting supported formats (e.g. mzXML)

The main use of this tool is to convert data from external sources to the formats used by OpenMS/TOPP. Maybe most importantly, data from MS experiments in a number of different formats can be converted to mzML, the canonical file format used by OpenMS/TOPP for experimental data. (mzML is the PSI approved format and supports traceability of analysis steps.)

Many different format conversions are supported, and some may be more useful than others. Depending on the file formats involved, information can be lost during conversion, e.g. when converting featureXML to mzData. In such cases a warning is shown.

The input and output file types are determined from the file extensions or from the first few lines of the files. If file type determination is not possible, the input or output file type has to be given explicitly.

Conversion with the same output as input format is supported. In some cases, this can be helpful to remove errors from files, to update file formats to new versions, or to check whether information is lost upon reading or writing.

Some information about the supported input types: mzML mzXML mzData mgf dta2d dta featureXML consensusXML ms2 fid/XMASS tsv peplist kroenik edta

See IDFileConverter for similar functionality for protein/peptide identification file formats.

The command line parameters of this tool are:

FileConverter -- Converts between different MS file formats.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  FileConverter <options>

Options (mandatory options marked with '*'):
  -in <file>*        Input file  (valid formats: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXM
                     L', 'consensusXML', 'ms2', 'fid', 'tsv', 'peplist', 'kroenik', 'edta')
  -in_type <type>    Input file type -- default: determined from file extension or content
                     (valid: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML'
                     , 'ms2', 'fid', 'tsv', 'peplist', 'kroenik', 'edta')
  -out <file>*       Output file  (valid formats: 'mzData', 'mzXML', 'mzML', 'dta2d', 'mgf', 'featureXML', 
                     'consensusXML', 'edta')
  -out_type <type>   Output file type -- default: determined from file extension or content
                     (valid: 'mzData', 'mzXML', 'mzML', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'edta
                     ')
                     
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
+FileConverterConverts between different MS file formats.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'FileConverter'
in input file input file*.mzData,*.mzXML,*.mzML,*.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,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta
out output file output file*.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta
out_type output file type -- default: determined from file extension or content
mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta
TIC_DTA2Dfalse Export the TIC instead of the entire experiment in mzML/mzData/mzXML -> DTA2D conversions.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
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5