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required parameter

advanced parameter

+IDMapperAssigns protein/peptide identifications to features or consensus features.

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

++1Instance '1' section for 'IDMapper'

id Protein/peptide identifications fileinput file*.idXML

in Feature map/consensus map fileinput file*.featureXML,*.consensusXML,*.mzq

out Output file (the format depends on the input file format).output file*.featureXML,*.consensusXML,*.mzq

rt_tolerance5 RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.
Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.0:∞

mz_tolerance20 m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.
Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value.0:∞

mz_measureppm Unit of 'mz_tolerance'.ppm,Da

mz_referenceprecursor Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',
masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.
('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)precursor,peptide

ignore_chargefalse For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.true,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

+++featureAdditional options for featureXML input

use_centroid_rtfalse Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces.true,false

use_centroid_mzfalse Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.
(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)true,false

+++consensusfeatureAdditional options for consensusXML input

use_subelementsfalse Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches.true,false