XFDR

Options

version

Version of the tool that generated this parameters file.

in_type

Type of input file provided with -in. If omitted, the file type is guessed from the file extension.

decoy_string

Prefix of decoy protein ids. The correspondig target protein id should be retrievable by deleting this prefix.

minborder

Filter for minimum precursor mass error (ppm) before FDR estimation. Values outside of the tolerance window of the original search will effectively disable this filter.

maxborder

Filter for maximum precursor mass error (ppm) before FDR estimation. Values outside of the tolerance window of the original search will effectively disable this filter.

mindeltas

Filter for delta score, 0 disables the filter. Minimum delta score required, hits are rejected if larger or equal. The delta score is a ratio of the score of a hit and the score of the next best hit to the same spectrum, so the value range is between 0 and 1 with 1.0 meaning the scores are equal and 0.5 meaning the next best score is half as high as the current one.

minionsmatched

Filter for minimum matched ions per peptide.

uniquexl

Calculate statistics based only on unique IDs. For a set of IDs from equal candidates (same pair of peptides, modifications and cross-linked positions), only the highest scoring hit will be considered. By default the score distribution will be estimated using all 1st ranked candidates.

no_qvalues

Do not transform simple FDR to q-values

minscore

Minimum score to be considered for FDR calculation. A number lower than the lowest score will effectively disable this filter.

binsize

Bin size for the cumulative histograms for score distributions. Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed. Should only be changed if the range of the main score changes or another score than the OpenPepXL score is used.

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)

Views

XFDR Std Output

The text sent to standard out during the execution of XFDR.

XFDR Error Output

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

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