SpectraSTSearchAdapter

Interface to the SEARCH Mode of the SpectraST executable

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)

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

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

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.)

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To use this node in KNIME, install the extension OpenMS from the below update site following our NodePit Product and Node Installation Guide:

v5.2

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

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, ZIB (GKN-Team) and the OpenMS Team

Plugin version: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-04-25

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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