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
- read the whole file into the OpenMS datastructures
- read only an index (read_memdump_idx) of the spectra and chromatograms and then use random-access to retrieve a specific spectra from the disk (read_memdump_spectra)
- Note
- This tool is experimental!
The command line parameters of this tool are:
OpenSwathMzMLFileCacher -- This tool caches the spectra and chromatogram data of an mzML to disk.
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:
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: 'tru
e', 'false')
-full_meta <type> Write full meta information into sqMass file (may require large amounts of memor
y) (default: 'true' valid: 'true', 'false')
Common UTIL 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
+OpenSwathMzMLFileCacherThis tool caches the spectra and chromatogram data of an mzML to disk.
version2.4.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathMzMLFileCacher'
in
Input mzML fileinput file*.mzML,*.sqMass
in_type
input file type -- default: determined from file extension or content
mzML,sqMass
out
Output fileoutput file*.mzML,*.sqMass
out_type
Output file type -- default: determined from file extension or content
Note: that not all conversion paths work or make sense.mzML,sqMass
convert_backfalse
Convert back to mzMLtrue,false
lossy_compressiontrue
Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data).true,false
full_metatrue
Write full meta information into sqMass file (may require large amounts of memory)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
lowmem_batchsize500
The batch size of the low memory conversion0:∞
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