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required parameter

advanced parameter

+RNPxlTool for RNP cross linking experiment analysis.

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'RNPxl'

in_mzML Input fileinput file*.mzML

length4 Oligonucleotide maximum length.

sequence Sequence to restrict the generation of oligonucleotide chains. (disabled for empty sequence)

target_nucleotides[A=C10H14N5O7P, C=C9H14N3O8P, G=C10H14N5O8P, U=C9H13N2O9P] 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[A->A, C->C, G->G, U->U] format: source->target e.g. A->A, ..., U->U, U->X

restrictions[A=0, C=0, U=0, G=0] format: target nucleotide=min_count: e.g U=1 if at least one U must be in the generated sequence.

modifications[-H2O, , -H2O-HPO3, -HPO3, -H2O+HPO3, +HPO3] format: empirical formula e.g -H2O, ..., H2O+PO3

peptide_mass_threshold600 Lower peptide mass (Da) threshold.

precursor_variant_mz_threshold260 Lower m/z (Th) threshold for precursor variant.

CysteineAdductfalse Use this flag if the +152 adduct is expected.true,false

in_OMSSA_ini Ini file for the OMSSA search engine
input file*.ini

in_fasta Fasta file for search result annotation
input file*.fasta

marker_ions_tolerance0.05 mz tolerance used to determine marker ions.

out_idXML idXML output file
output file*.idXML

out_csv csv output file
output file*.csv

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false