IconFidoAdapter0 ×

Generic Workflow Nodes for KNIME: OpenMS version 2.3.0.201712211252 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Runs the protein inference engine Fido.

Web Documentation for 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
Overwrite 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)

Input Ports

Input: identification results [idXML]

Output Ports

Output: identification results with scored/grouped proteins [idXML]

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: OpenMS from the following update site:

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