OpenSwathChromatogramExtractor

Options

version

Version of the tool that generated this parameters file.

min_upper_edge_dist

Minimal distance to the edge to still consider a precursor, in Thomson

rt_window

Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side.

ion_mobility_window

Extraction window in ion mobility dimension (in milliseconds). This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side.

mz_window

Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size, e.g. 100 ppm would extract 50 ppm on either side.

ppm

m/z extraction_window is in ppm

is_swath

Set this flag if the data is SWATH data

extract_MS1

Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)

extraction_function

Function used to extract the signal

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)

type

Type of model

symmetric_regression

Only for 'linear' model: Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.

Views

OpenSwathChromatogramExtractor Std Output

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

OpenSwathChromatogramExtractor Error Output

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

Links

• No links available

Developers