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SpectraSTSearchAdapter

Generic Workflow Nodes for KNIME: OpenMS version 2.6.0.202009301213 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Interface to the SEARCH Mode of the SpectraST executable

Web Documentation for SpectraSTSearchAdapter

Options

version
Version of the tool that generated this parameters file.
sequence_database_type
Specify type of sequence database
precursor_mz_tolerance
m/z (in Th) tolerance within which candidate entries are compared to the query. Monoisotopic mass is assumed.
use_isotopically_averaged_mass
Use isotopically averaged mass instead of monoisotopic mass
use_all_charge_states
Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum
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)

Input Ports

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Path to the SpectraST executable to use; may be empty if the executable is globally available. []
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File names(s) of spectra to be searched. [mzML,mzXML,mzData,mgf,dta,msp]
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Specify library file. [splib]
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The sequence database. [fasta,opt.]
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Only search a subset of the query spectra in the search file [txt,dat,opt.]
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Read search options from file. All options set in the file will be overridden by command-line options, if specified. [params,opt.]
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Specify name of user-defined modifications file. Default is "spectrast.usermods". [,opt.]

Output Ports

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Output files. Make sure to specify one output file for each input file [txt,tsv,xml,pepXML,html]

Views

SpectraSTSearchAdapter Std Output
The text sent to standard out during the execution of SpectraSTSearchAdapter.
SpectraSTSearchAdapter Error Output
The text sent to standard error during the execution of SpectraSTSearchAdapter. (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

A zipped version of the software site can be downloaded here.

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Developers

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