AssayGeneratorMetaboSirius

Options

version

Version of the tool that generated this parameters file.

ambiguity_resolution_mz_tolerance

Mz tolerance for the resolution of identification ambiguity over multiple files

ambiguity_resolution_mz_tolerance_unit

Unit of the ambiguity_resolution_mz_tolerance

ambiguity_resolution_rt_tolerance

RT tolerance in seconds for the resolution of identification ambiguity over multiple files

total_occurrence_filter

Filter compound based on total occurrence in analysed samples

fragment_annotation_score_threshold

Filters annotations based on the explained intensity of the peaks in a spectrum

method

Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used).

use_exact_mass

Use exact mass for precursor and fragment annotations

exclude_ms2_precursor

Excludes precursor in ms2 from transition list

use_known_unknowns

Use features without identification information

min_transitions

Minimal number of transitions

max_transitions

Maximal number of transitions

transition_threshold

Further transitions need at least x% of the maximum intensity (default 5%)

min_fragment_mz

Minimal m/z of a fragment ion choosen as a transition

max_fragment_mz

Maximal m/z of a fragment ion choosen as a transition

decoy_generation

Decoys will be generated using the fragmentation tree re-rooting approach. This option does only work in combination with the fragment annotation via Sirius.

decoy_generation_method

Uses different methods for decoy generation. Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping target/decoy fragments by adding -CH2 mass to the overlapping decoy fragments. 'generate_missing_decoys' will add a -CH2 mass shift to the target fragments and use them as decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, generate_missing_decoys).

decoy_resolution_mz_tolerance

Mz tolerance for the resolution of overlapping m/z values for targets and decoys of one compound.

decoy_resolution_mz_tolerance_unit

Unit of the decoy_resolution_mz_tolerance

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

AssayGeneratorMetaboSirius Std Output

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

AssayGeneratorMetaboSirius Error Output

The text sent to standard error during the execution of AssayGeneratorMetaboSirius. (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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