OpenMS
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Serialize a spectra and/or chromatogram mzML file
This class will serialize a spectra and/or chromatogram mzML file and store it in a binary format that contains ONLY the spectra and chromatogram data (no metadata).
This is implemented using the write_memdump and read_memdump functions. For reading there are 2 options
The command line parameters of this tool are:
OpenSwathMzMLFileCacher -- Caches the spectra and chromatogram data of an mzML to disk. Full documentation: http://www.openms.de/doxygen/release/3.3.0/html/TOPP_OpenSwathMzMLFileCacher.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 To cite OpenMS: + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7. Usage: OpenSwathMzMLFileCacher <options> Options (mandatory options marked with '*'): -in <file>* Input mzML file (valid formats: 'mzML', 'sqMass') -in_type <type> Input file type -- default: determined from file extension or content (valid: 'mzML', 'sqMass') -out <file>* Output file (valid formats: 'mzML', 'sqMass') -out_type <type> Output file type -- default: determined from file extension or content Note: that not all conversion paths work or make sense. (valid: 'mzML', 'sqMass' ) -convert_back Convert back to mzML -lossy_compression <type> Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data). (default: 'true') (valid: 'true', 'false') -full_meta <type> Write full meta information into sqMass file (may require large amounts of memor y) (default: 'true') (valid: 'true', 'false') 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: