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FileConverter

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Converts between different MS file formats.

Web Documentation for FileConverter

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.
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'.
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.
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).
change_im_format
[mzML output only] How to store ion mobility scans (none: no change in format, multiple: store each frame as multiple scans, one per drift time value, single: store whole frame as single scan with IM values in a FloatDataArray
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.
no_peak_picking
Disables vendor peak picking for raw files.
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)

Input Ports

Icon
Input file to convert. [mzML,mzXML,mgf,raw,cachedMzML,mzData,dta,dta2d,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta]
Icon
The .NET framework executable. Only required on linux and mac. [,opt.]
Icon
The ThermoRawFileParser executable. [exe,opt.]

Output Ports

Icon
Output file [mzML,mzXML,cachedMzML,mgf,featureXML,consensusXML,edta,mzData,dta2d,csv]

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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Developers

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