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TextExporter

Generic Workflow Nodes for KNIME: OpenMS version 2.4.0.201810261314 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

Exports various XML formats to a text file.

Web Documentation for TextExporter

Options

version
Version of the tool that generated this parameters file.
separator
The used separator character(s); if not set the 'tab' character is used
replacement
Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'
quoting
Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, 'escape' for quoting with backslash-escaping of embedded quotes
no_ids
Suppresses output of identification data.
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)
minimal
Set this flag to write only three attributes: RT, m/z, and intensity.
add_metavalues
Add columns for meta values which occur with a certain frequency (0-100%). Set to -1 to omit meta values (default).
proteins_only
Set this flag if you want only protein information from an idXML file
peptides_only
Set this flag if you want only peptide information from an idXML file
first_dim_rt
If this flag is set the first_dim RT of the peptide hits will also be printed (if present).
add_metavalues
Add columns for meta values which occur with a certain frequency (0-100%). Set to -1 to omit meta values (default).
add_hit_metavalues
Add columns for meta values which occur with a certain frequency (0-100%). Set to -1 to omit meta values (default).
sorting_method
Sorting options can be combined. The precedence is: sort_by_size, sort_by_maps, sorting_method
sort_by_maps
Apply a stable sort by the covered maps, lexicographically
sort_by_size
Apply a stable sort by decreasing size (i.e., the number of elements)

Input Ports

Input file [featureXML,consensusXML,idXML,mzML]

Output Ports

Output file (mandatory for featureXML and idXML) [csv,Inactive]
Output file for centroids of consensus features [csv,Inactive]
Output file for elements of consensus features [csv,Inactive]
Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing) [csv,Inactive]

Views

TextExporter Std Output
The text sent to standard out during the execution of TextExporter.
TextExporter Error Output
The text sent to standard error during the execution of TextExporter. (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

Installation

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

KNIME 3.7
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