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XFDR

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Calculates false discovery rate estimates on crosslink identifications

Web Documentation for 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
Overwrite tool specific checks.
test
Enables the test mode (needed for internal use only)

Input Ports

Icon
Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format (as produced by OpenPepXL) [xml,idXML,mzid,xquest.xml,opt.]

Output Ports

Icon
Output as idXML file [idXML]
Icon
Output as mzIdentML file [mzid]
Icon
Output as xquest.xml file [xquest.xml]

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2
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