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IDFileConverter

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Converts identification engine file formats.

Web Documentation for IDFileConverter

Options

version
Version of the tool that generated this parameters file.
out_type
Output file type (default: determined from file extension)
mz_name
[pepXML only] Experiment filename/path (extension will be removed) to match in the pepXML file ('base_name' attribute). Only necessary if different from 'mz_file'.
peptideprophet_analyzed
[pepXML output only] Write output in the format of a PeptideProphet analysis result. By default a 'raw' pepXML is produced that contains only search engine results.
score_type
[Percolator only] Which of the Percolator scores to report as 'the' score for a peptide hit
ignore_proteins_per_peptide
[Sequest only] Workaround to deal with .out files that contain e.g. "+1" in references column, but do not list extra references in subsequent lines (try -debug 3 or 4)
scan_regex
[Mascot, pepXML, Percolator only] Regular expression used to extract the scan number or retention time. See documentation for details.
no_spectra_data_override
[+mz_file only] Setting this flag will avoid overriding 'spectra_data' in ProteinIdentifications if mz_file is given and 'spectrum_reference's are added/updated. Use only if you are sure it is absolutely the same mz_file as used for identification.
add_ionmatch_annotation
[+mz_file only] Will annotate the contained identifications with their matches in the given mz_file. Will take quite some while. Match tolerance is .4
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

Input file or directory containing the data to convert. This may be:#br#- a single file in a multi-purpose XML format (.pepXML, .protXML, .idXML, .mzid),#br#- a single file in a search engine-specific format (Mascot: .mascotXML, OMSSA: .omssaXML, X! Tandem: .xml, Percolator: .psms, xQuest: .xquest.xml),#br#- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits),#br#- for Sequest results, a directory containing .out files.#br# [pepXML,protXML,mascotXML,omssaXML,xml,psms,tsv,idXML,mzid,xquest.xml]
[pepXML, Sequest, Mascot, X! Tandem, mzid, Percolator only] Retention times and native spectrum ids (spectrum_references) will be looked up in this file [mzML,mzXML,mzData,opt.]

Output Ports

Output file [idXML,mzid,pepXML,FASTA,xquest.xml]

Views

IDFileConverter Std Output
The text sent to standard out during the execution of IDFileConverter.
IDFileConverter Error Output
The text sent to standard error during the execution of IDFileConverter. (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 Generic Workflow Nodes for KNIME: OpenMS from the following update site:

KNIME 4.0
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