Perform preotein-RNA cross-linking experiments.
| pot. predecessor tools |  RNPxl   | pot. successor tools | 
| RNPxlXICFilter | - | 
The command line parameters of this tool are:
RNPxl -- Tool for RNP cross linking experiment analysis.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  RNPxl <options>
Options (mandatory options marked with '*'):
  -in_mzML <file>*                             Input file (valid formats: 'mzML')
  -length                                      Oligonucleotide maximum length. (default: '4')
  -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 (default: '[A=C
                                               10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P]')
  -mapping                                     Format: source->target e.g. A->A, ..., U->U, U->X (default: 
                                               '[A->A C->C G->G U->U]')
  -restrictions                                Format: target nucleotide=min_count: e.g U=1 if at least one 
                                               U must be in the generated sequence. (default: '[A=0 C=0 U=0
                                               G=0]')
  -modifications                               Format: empirical formula e.g -H2O, ..., H2O+PO3 (default: 
                                               '[-H2O  -H2O-HPO3 -HPO3 -H2O+HPO3 +HPO3]')
  -peptide_mass_threshold <threshold>          Lower peptide mass (Da) threshold. (default: '600')
  -precursor_variant_mz_threshold <threshold>  Lower m/z (Th) threshold for precursor variant. (default: '260
                                               ')
  -CysteineAdduct                              Use this flag if the +152 adduct is expected.
  -in_OMSSA_ini <file>*                        Ini file for the OMSSA search engine
                                               (valid formats: 'ini')
  -in_fasta <file>*                            Fasta file for search result annotation
                                               (valid formats: 'fasta')
  -marker_ions_tolerance <tolerance>           Mz tolerance used to determine marker ions. (default: '0.05')
  -out_idXML <file>*                           IdXML output file
                                               (valid formats: 'idXML')
  -out_csv <file>*                             Csv output file
                                               (valid formats: 'csv')
                                               
Common UTIL options:
  -ini <file>                                  Use the given TOPP INI file
  -threads <n>                                 Sets the number of threads allowed to be used by the TOPP tool
                                               (default: '1')
  -write_ini <file>                            Writes the default configuration file
  --help                                       Shows options
  --helphelp                                   Shows all options (including advanced)
INI file documentation of this tool:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |