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FidoAdapter

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.
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)

Input Ports

: Input: identification results [idXML]

Output Ports

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

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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.)

Workflows

Developers

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Installation

To use this node in KNIME, install the extension OpenMSThirdparty 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 OpenMSThirdparty Team

Plugin version: 3.0.0.202307112039

On NodePit since: 2023-12-06

Last update: 2024-12-18

KNIME versions: From v5.1 to v5.3

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