Legend:
required parameter
advanced parameter
+MapRTTransformerApplies retention time transformations to maps.
version1.10.0
Version of the tool that generated this parameters file.
++1Instance '1' section for 'MapRTTransformer'
in[]
Input files to transform (separated by blanks)input file*.mzML,*.featureXML,*.consensusXML,*.idXML
out[]
Output files separated by blanks. Either this option or 'trafo_out' have to be provided. They can be used together.output file*.mzML,*.featureXML,*.consensusXML,*.idXML
trafo_in[]
Transformations to apply (files separated by blanks)input file*.trafoXML
trafo_out[]
Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together.output file*.trafoXML
invertfalse
Invert transformations (approximatively) before applying themtrue,false
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
typenone
Type of modelnone,linear,b_spline,interpolated
++++linearParameters for 'linear' model
symmetric_regressionfalse
Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.true,false
++++b_splineParameters for 'b_spline' model
num_breakpoints5
Number of breakpoints of the cubic spline in the smoothing step. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape.2:∞
break_positionsuniform
How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval.uniform,quantiles
++++interpolatedParameters for 'interpolated' model
interpolation_typecspline
Type of interpolation to apply.linear,cspline,akima