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+OpenSwathChromatogramExtractorExtract chromatograms (XIC) from a MS2 map file.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathChromatogramExtractor'

in[] Input files separated by blankinput file*.mzML

tr transition file ('TraML' or 'csv')input file*.csv,*.traML

rt_norm RT normalization file (how to map the RTs of this run to the ones stored in the library)input file*.trafoXML

out output fileoutput file*.mzML

min_upper_edge_dist0 Minimal distance to the edge to still consider a precursor, in Thomson

extraction_window0.05 Extraction window used (in Thomson, to use ppm see -ppm flag)0:∞

rt_extraction_window-1 Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution).

is_swathfalse Set this flag if the data is SWATH datatrue,false

ppmfalse extraction_window is in ppmtrue,false

extraction_functiontophat Function used to extract the signaltophat,bartlett

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

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

+++modelOptions to control the modeling of retention time transformations from data

typelinear Type of modellinear,b_spline,interpolated

symmetric_regressionfalse Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.true,false

num_breakpoints5 Only for 'b_spline' model: Number of breakpoints of the cubic spline in the smoothing step. The breakpoints are spaced uniformly on the retention time interval. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape.2:∞

interpolation_typecspline Only for 'interpolated' model: Type of interpolation to apply.