OpenMS
2.4.0

Applies retention time transformations to maps.
potential predecessor tools  MapRTTransformer  potential successor tools 
MapAlignerIdentification (or another alignment algorithm)  FeatureLinkerUnlabeled or FeatureLinkerUnlabeledQT 
This tool can apply retention time transformations to different types of data (mzML, featureXML, consensusXML, and idXML files). The transformations might have been generated by a previous invocation of one of the MapAligner tools (linked below). However, the trafoXML file format is not very complicated, so it is relatively easy to write (or generate) your own files. Each input file will give rise to one output file.
With this tool it is also possible to invert transformations, or to fit a different model than originally specified to the retention time data in the transformation files. To fit a new model, choose a value other than "none" for the model type (see below).
Original retention time values can be kept as meta data. With the option store_original_rt
, meta values with the name "original_RT" and the original retention time will be created for every major data element (spectrum, chromatogram, feature, consensus feature, peptide identification), unless they already exist  "original_RT" values from a previous invocation will not be overwritten.
Since OpenMS 1.8, the extraction of data for the alignment has been separate from the modeling of RT transformations based on that data. It is now possible to use different models independently of the chosen algorithm. The different available models are:
The following parameters control the modeling of RT transformations (they can be set in the "model" section of the INI file):
Name  Type  Default  Restrictions  Description 

type  string  none  none, linear, b_spline, lowess, interpolated  Type of model 
linear:symmetric_regression  string  false  true, false  Perform linear regression on 'y  x' vs. 'y + x', instead of on 'y' vs. 'x'. 
linear:x_weight  string  1/x, 1/x2, ln(x),  Weight x values  
linear:y_weight  string  1/y, 1/y2, ln(y),  Weight y values  
linear:x_datum_min  float  1e15  Minimum x value  
linear:x_datum_max  float  1e+15  Maximum x value  
linear:y_datum_min  float  1e15  Minimum y value  
linear:y_datum_max  float  1e+15  Maximum y value  
b_spline:wavelength  float  0  min: 0  Determines the amount of smoothing by setting the number of nodes for the Bspline. The number is chosen so that the spline approximates a lowpass 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. 
b_spline:num_nodes  int  5  min: 0  Number of nodes for Bspline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing. 
b_spline:extrapolate  string  linear  linear, b_spline, constant, global_linear  Method to use for extrapolation beyond the original data range. 'linear': Linear extrapolation using the slope of the Bspline at the corresponding endpoint. 'b_spline': Use the Bspline (as for interpolation). 'constant': Use the constant value of the Bspline 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). 
b_spline:boundary_condition  int  2  min: 0 max: 2  Boundary condition at Bspline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero) 
lowess:span  float  0.666666666666667  min: 0 max: 1  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. 
lowess:num_iterations  int  3  min: 0  Number of robustifying iterations for lowess fitting. 
lowess:delta  float  1  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.  
lowess:interpolation_type  string  cspline  linear, cspline, akima  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 
lowess:extrapolation_type  string  fourpointlinear  twopointlinear, fourpointlinear, globallinear  Method to use for extrapolation outside the data range. 'twopointlinear': Uses a line through the first and last point to extrapolate. 'fourpointlinear': Uses a line through the first and second point to extrapolate in front and and a line through the last and secondtolast point in the end. 'globallinear': Uses a linear regression to fit a line through all data points and use it for interpolation. 
interpolated:interpolation_type  string  cspline  linear, cspline, akima  Type of interpolation to apply. 
interpolated:extrapolation_type  string  twopointlinear  twopointlinear, fourpointlinear, globallinear  Type of extrapolation to apply: twopointlinear: use the first and last data point to build a single linear model, fourpointlinear: build two linear models on both ends using the first two / last two points, globallinear: use all points to build a single linear model. Note that globallinear may not be continuous at the border. 
out
or trafo_out
has to be provided. They can be used together.The command line parameters of this tool are:
MapRTTransformer  Applies retention time transformations to maps. Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible opensource software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741748. doi:10.1038/nmeth.3959. Usage: MapRTTransformer <options> This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript ion or use the helphelp option. Options (mandatory options marked with '*'): in <file> Input file to transform (separated by blanks) (valid formats: 'mzML', 'featureXML', 'consensusXML', 'idXML') out <file> Output file (same file type as 'in'). Either this option or 'trafo_out' has to be prov ided; they can be used together. (valid formats: 'mzML', 'featureXML', 'consensusXML', 'idXML') trafo_in <file>* Transformation to apply (valid formats: 'trafoXML') trafo_out <file> Transformation output file. Either this option or 'out' has to be provided; they can be used together. (valid formats: 'trafoXML') invert Invert transformation (approximatively) before applying it store_original_rt Store the original retention times (before transformation) as meta data in the output file Common TOPP options: ini <file> Use the given TOPP INI file threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1') write_ini <file> Writes the default configuration file help Shows options helphelp Shows all options (including advanced) The following configuration subsections are valid:  model Options to control the modeling of retention time transformations from data You can write an example INI file using the 'write_ini' option. Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor. Have a look at the OpenMS documentation for more information.
INI file documentation of this tool: