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. mzML)

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.)

For MaxQuant-flavoured mzXML the use of the advanced option '-force_MaxQuant_compatibility' is recommended.

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 (e.g. the index), 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

Note: 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: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06
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:
  FileConverter <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')
  -out <file>*       Output file (valid formats: 'mzData', 'mzXML', 'mzML', 'cachedMzML', 'dta2d', 'mgf', 
                     'featureXML', 'consensusXML', 'edta', 'csv')
                     
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.

version2.4.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'FileConverter'

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

UID_postprocessingensure unique ID post-processing for output data.
'none' keeps current IDs even if invalid.
'ensure' keeps current IDs but reassigns invalid ones.
'reassign' assigns new unique IDs.none,ensure,reassign

out Output fileoutput file*.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv

out_type Output file type -- default: determined from file extension or content
Note: that not all conversion paths work or make sense.mzData,mzXML,mzML,cachedMzML,dta2d,mgf,featureXML,consensusXML,edta,csv

TIC_DTA2Dfalse Export the TIC instead of the entire experiment in mzML/mzData/mzXML -> DTA2D conversions.true,false

MGF_compactfalse Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)true,false

force_MaxQuant_compatibilityfalse [mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'.true,false

convert_to_chromatogramsfalse [mzML output only] Assumes that the provided spectra represent data in SRM mode or targeted MS1 mode and converts them to chromatogram data.true,false

force_TPP_compatibilityfalse [mzML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP).true,false

write_scan_indextrue Append an index when writing mzML or mzXML files. Some external tools might rely on it.true,false

lossy_compressionfalse Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data).true,false

lossy_mass_accuracy-1 Desired (absolute) m/z accuracy for lossy compression (e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy).

process_lowmemoryfalse Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).
Note: this flag will prevent conversion from spectra to chromatograms.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 Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false