RawFileConverter

Options

version

Version of the tool that generated this parameters file.

in_type

Input file type -- default: determined from file extension or content

UID_postprocessing

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.

out_type

Output file type -- default: determined from file extension or content Note: that not all conversion paths work or make sense.

TIC_DTA2D

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

MGF_compact

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

force_MaxQuant_compatibility

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

force_TPP_compatibility

[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).

convert_to_chromatograms

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

write_scan_index

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

lossy_compression

Use numpress compression to achieve optimally small file size using linear compression for m/z domain and slof for intensity and float data arrays (attention: may cause small loss of precision; only for mzML data).

lossy_mass_accuracy

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_lowmemory

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.

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

no_peak_picking

Disables vendor peak picking for raw files.

no_zlib_compression

Disables zlib compression for raw file conversion. Enables compatibility with some tools that do not support compressed input files, e.g. X!Tandem.

include_noise

Include noise data in mzML output.

Views

RawFileConverter Std Output

The text sent to standard out during the execution of RawFileConverter.

RawFileConverter Error Output

The text sent to standard error during the execution of RawFileConverter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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