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RNPxl

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

Tool for RNP cross linking experiment analysis.

Web Documentation for RNPxl

Options

version
Version of the tool that generated this parameters file.
length
Oligonucleotide maximum length.
sequence
Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence)
target_nucleotides
format: target nucleotide=empirical formula of nucleoside monophosphate e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU or e.g. Y=C10H14N5O7PS where Y represents tG
mapping
format: source->target e.g. A->A, ..., U->U, U->X
restrictions
format: target nucleotide=min_count: e.g U=1 if at least one U must be in the generated sequence.
modifications
format: empirical formula e.g -H2O, ..., H2O+PO3
peptide_mass_threshold
Lower peptide mass (Da) threshold.
precursor_variant_mz_threshold
Lower m/z (Th) threshold for precursor variant.
CysteineAdduct
Use this flag if the +152 adduct is expected.
continue
Do not recreate intermediate files to continue after unexpected crash.
marker_ions_tolerance
mz tolerance used to determine marker ions.
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)

Input Ports

Input file [mzML]
Ini file for the OMSSA search engine#br# [ini]
Fasta file for search result annotation#br# [fasta]

Output Ports

idXML output file#br# [idXML]
csv output file#br# [csv]

Views

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

Best Friends (Incoming)

Update Site

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