OpenSwathConfidenceScoring

Compute confidence scores for OpenSwath results

Web Documentation for OpenSwathConfidenceScoring

Options

version
Version of the tool that generated this parameters file.
decoys
Number of decoy assays to select from the library for every true assay (0 for "all")
transitions
Number of transitions per feature to consider (highest intensities first; 0 for "all")
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)
intercept
Intercept term
delta_rt
Coefficient of retention time difference
dist_int
Coefficient of intensity distance

Input Ports

Icon
Input file (OpenSwath results) [featureXML]
Icon
Assay library [traML]
Icon
Retention time transformation [trafoXML,opt.]

Output Ports

Icon
Output file (results with confidence scores) [featureXML]

Popular Predecessors

  • No recommendations found

Popular Successors

  • No recommendations found

Views

OpenSwathConfidenceScoring Std Output
The text sent to standard out during the execution of OpenSwathConfidenceScoring.
OpenSwathConfidenceScoring Error Output
The text sent to standard error during the execution of OpenSwathConfidenceScoring. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

  • No workflows found

Further Links

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.