FeatureLinkerUnlabeledQT

Groups corresponding features from multiple maps.

Web Documentation for FeatureLinkerUnlabeledQT

Options

version
Version of the tool that generated this parameters file.
keep_subelements
For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.
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
Overrides tool-specific checks
test
Enables the test mode (needed for internal use only)
use_identifications
Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account).
nr_partitions
How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution).
min_nr_diffs_per_bin
If IDs are used: How many differences from matching IDs should be used to calculate a linking tolerance for unIDed features in an RT region. RT regions will be extended until that number is reached.
min_IDscore_forTolCalc
If IDs are used: What is the minimum score of an ID to assume a reliable match for tolerance calculation. Check your current score type!
noID_penalty
If IDs are used: For the normalized distances, how high should the penalty for missing IDs be? 0 = no bias, 1 = IDs inside the max tolerances always preferred (even if much further away).
ignore_charge
false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state
ignore_adduct
true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts
max_difference
Never pair features with a larger RT distance (in seconds).
exponent
Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
weight
Final RT distances are weighted by this factor
max_difference
Never pair features with larger m/z distance (unit defined by 'unit')
unit
Unit of the 'max_difference' parameter
exponent
Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
weight
Final m/z distances are weighted by this factor
exponent
Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
weight
Final intensity distances are weighted by this factor
log_transform
Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))

Input Ports

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input files separated by blanks [featureXML,consensusXML]
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input file containing the experimental design [tsv,opt.]

Output Ports

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Output file [consensusXML]

Views

FeatureLinkerUnlabeledQT Std Output
The text sent to standard out during the execution of FeatureLinkerUnlabeledQT.
FeatureLinkerUnlabeledQT Error Output
The text sent to standard error during the execution of FeatureLinkerUnlabeledQT. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

Further Links

Developers

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