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required parameter
advanced parameter
+RNPxlTool for RNP cross linking experiment analysis.
version2.0.0
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
continuefalse
Do not recreate intermediate files to continue after unexpected crash.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
forcefalse
Overwrite tool specific checks.true,false
testfalse
Enables the test mode (needed for internal use only)true,false