Performs an ProteinIdentification with PILIS
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PILISModelTrainer | ConsensusID | |
IDMapper |
The PILISIdentification TOPP tool performs a ProteinIdentification run with the PILIS ProteinIdentification engine. As input the file given in the in parameters is used. The identifications are written into an idXML file given in the out parameter. Additionally the model_file must be specified. To perform a search also a peptide database file should be used,given in the peptide_db_file parameter. This should contain a peptide in a separate line, either only the sequence or additionally with weight and charge in the second and third column.
The command line parameters of this tool are:
PILISIdentification -- performs a peptide/protein identification with the PILIS engine Version: 2.0.0 May 16 2015, 09:22:21, Revision: GIT-NOTFOUND Usage: PILISIdentification <options> Options (mandatory options marked with '*'): -in <file>* Input file in MzML format (valid formats: 'mzML') -out <file>* Output file in idXML format (valid formats: 'idXML') -model_file <file* The model file of the PILISModel -peptide_db_file <file>* A file which should contain peptides in the format DFPIANGER 1019.09 1 where the first column is the peptide, the second the m /z the third the charge. As a alternative the sequence fil e may contain only peptide sequences each in a separate l ine repectively -precursor_mass_tolerance <tol> The precursor mass tolerance (default: '2') -peak_mass_tolerance <tol> The peak mass tolerance (default: '1') -max_pre_candidates <int> Number of candidates that are used for precise scoring (default: '200') -max_candidates <int> Number of candidates that are reported by PILIS (default : '20') -upper_mz <double> Upper mz interval endpoint (default: '2000') -lower_mz <double> Lower mz interval endpoint (default: '200') -fixed_modifications <mods> Monoisotopic_mass@residues e.g.: 57.021464@C Parameters of PILISModel: -model:charge_directed_threshold <double> Bla (default: '0.3') -model:charge_remote_threshold <double> Bla (default: '0.2') -model:charge_loss_factor <double> Bla (default: '0.5') -model:min_y_ion_intensity <double> (default: '0.2') -model:min_b_ion_intensity <double> (default: '0.15') -model:min_a_ion_intensity <double> (default: '0.05') -model:min_y_loss_intensity <double> (default: '0.05') -model:min_b_loss_intensity <double> (default: '0.02') -model:visible_model_depth <int> Bla (default: '30') -model:model_depth <int> Bla (default: '4') Parameters of PILISScoring: -scoring:use_local_scoring ... -scoring:do_not_use_evalue_scoring ... -scoring:survival_function_bin_size <int> ... (default: '20') -scoring:global_linear_fitting_threshold <double> ... (default: '0.1') -scoring:local_linear_fitting_threshold <double> ... (default: '0.5') Common TOPP 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 2.0.0 | Documentation generated on Sat May 16 2015 16:13:42 using doxygen 1.8.9.1 |