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required parameter

advanced parameter

+MapAlignerPoseClusteringCorrects retention time distortions between maps using a pose clustering approach.

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

++1Instance '1' section for 'MapAlignerPoseClustering'

in[] Input files separated by blanks (all must have the same file type)input file*.mzML,*.featureXML

out[] Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together.output file*.mzML,*.featureXML

trafo_out[] Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together.output file*.trafoXML

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

+++referenceOptions to define a reference file (use either 'file' or 'index', not both; if neither is given 'index' is used).

file File to use as reference (same file format as input files required)input file*.mzML,*.featureXML

index0 Use one of the input files as reference ('1' for the first file, etc.).
If '0', no explicit reference is set - the algorithm will select a reference.0:∞

+++algorithmAlgorithm parameters section

max_num_peaks_considered1000 The maximal number of peaks/features to be considered per map. To use all, set to '-1'.-1:∞

++++superimposer

mz_pair_max_distance0.5 Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.0:∞

rt_pair_distance_fraction0.1 Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). 0:1

num_used_points2000 Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.-1:∞

scaling_bucket_size0.005 The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs.0:∞

shift_bucket_size3 The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans.0:∞

max_shift1000 Maximal shift which is considered during histogramming. This applies for both directions.0:∞

max_scaling2 Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this.1:∞

dump_buckets [DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically.

dump_pairs [DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically.

++++pairfinder

second_nearest_gap2 The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself.1:∞

use_identificationsfalse Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).true,false

ignore_chargefalse Compare features normally even if their charge states are differenttrue,false

+++++distance_RTDistance component based on RT differences

max_difference100 Maximum allowed difference in RT in seconds0:∞

exponent1 Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)0:∞

weight1 RT distances are weighted by this factor0:∞

+++++distance_MZDistance component based on m/z differences

max_difference0.3 Maximum allowed difference in m/z (unit defined by 'unit')0:∞

unitDa Unit of the 'max_difference' parameterDa,ppm

exponent2 Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)0:∞

weight1 m/z distances are weighted by this factor0:∞

+++++distance_intensityDistance component based on differences in relative intensity

exponent1 Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)0:∞

weight0 Distances based on relative intensity are weighted by this factor0:∞