FidoAdapter

Options

version

Version of the tool that generated this parameters file.

separate_runs

Process multiple protein identification runs in the input separately, don't merge them. Merging results in loss of descriptive information of the single protein identification runs.

keep_zero_group

Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)

greedy_group_resolution

Post-process Fido output with greedy resolution of shared peptides based on the protein probabilities. Also adds the resolved ambiguity groups to output.

no_cleanup

Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)

all_PSMs

Consider all PSMs of each peptide, instead of only the best one

group_level

Perform inference on protein group level (instead of individual protein level). This will lead to higher probabilities for (bigger) protein groups.

accuracy

Accuracy level of start parameters. There is a trade-off between accuracy and runtime. Empty uses the default ('best').

log2_states

Binary logarithm of the max. number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18).

log2_states_precalc

Like 'log2_states', but allows to set a separate limit for the precalculation

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)

protein

Protein prior probability ('gamma' parameter)

peptide

Peptide emission probability ('alpha' parameter)

spurious

Spurious peptide identification probability ('beta' parameter)

Views

FidoAdapter Std Output

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

FidoAdapter Error Output

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