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MapRTTransformer

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Applies retention time transformations to maps.

Web Documentation for MapRTTransformer

Options

version
Version of the tool that generated this parameters file.
invert
Invert transformation (approximatively) before applying it
store_original_rt
Store the original retention times (before transformation) as meta data in the output file
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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)
type
Type of model
symmetric_regression
Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.
x_weight
Weight x values
y_weight
Weight y values
x_datum_min
Minimum x value
x_datum_max
Maximum x value
y_datum_min
Minimum y value
y_datum_max
Maximum y value
wavelength
Determines the amount of smoothing by setting the number of nodes for the B-spline. The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points.
num_nodes
Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing.
extrapolate
Method to use for extrapolation beyond the original data range. 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range).
boundary_condition
Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)
span
Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.
num_iterations
Number of robustifying iterations for lowess fitting.
delta
Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.
interpolation_type
Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation
extrapolation_type
Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.
interpolation_type
Type of interpolation to apply.
extrapolation_type
Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border.

Input Ports

Icon
Input file to transform (separated by blanks) [mzML,featureXML,consensusXML,idXML,opt.]
Icon
Transformation to apply [trafoXML]

Output Ports

Icon
Output file (same file type as 'in'). This option or 'trafo_out' has to be provided; they can be used together. [mzML,featureXML,consensusXML,idXML]
Icon
Transformation output file. This option or 'out' has to be provided; they can be used together. [trafoXML]

Views

MapRTTransformer Std Output
The text sent to standard out during the execution of MapRTTransformer.
MapRTTransformer Error Output
The text sent to standard error during the execution of MapRTTransformer. (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
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