Peptideshaker github zip file#
(*) Not mandatory if these files are part of a zip file input with the identification files. Generated using the GUI or via IdentificationParametersCLI.Īlternatively, IdentificationParametersCLI parameters can be passed directly.
id_params (*) The identification parameters file (.par).
spectrum_files (*) The spectrum files (mgf or mzML format) in a comma separated list or anĮntire folder. identification_files Identification files in a comma separated list, as compressed zip file, fasta_file (*) The complete path to the FASTA file. Mandatory parameters -reference The reference for the project. Standard command line java -cp PeptideShaker-X.Y.Z.jar eu. In distributed setups, we recommend keeping a clean copy of PeptideShaker, and distribute it to the different workers prior to execution. It is thus important to use a single instance of PeptideShakerCLI at a time. Note that PeptideShaker back-end relies on a database allowing only a single open connection at a time. Temporary folders used in the processing can be set via PathSettingsCLI. Alternatively, the parameters can be passed directly to PeptideShakerCLI by using the command line arguments of the IdentificationParametersCLI. Identification parameter files are in the json format and can be created in the graphical user interface, using the IdentificationParametersCLI, or using third party tools. Identification parameters for use in PeptideShakerCLI can be provided as a file. Note that ReportCLI, FollowUpCLI, MzidCLI and PathSettingsCLI options can also be appended directly to PeptideShakerCLI command lines.Īll command line options have the same overall structure and only differ in the features and parameters available. E) PathSettingsCLI - set the paths to use.C) FollowUpCLI - export for follow up analysis.B) ReportCLI - identification results exports.There are six main sections to this page: The PeptideShaker command line interface can be used to process identification files and output identification results in various formats. To add custom reports see Export > Identification Features > Reports in PeptideShaker.PeptideShakerCLI PeptideShaker Command Line Interface gzip Indicates whether the report should be compressed. documentation Comma separated list of types of report documentation to export. report_prefix Prefix added to the report file name. reports Comma separated list of types of report to export.Ĥ: Default PSM Report with non-validated matches,ĥ: Default Peptide Phosphorylation Report,ħ: Default Peptide Report with non-validated matches,Ĩ: Default Protein Phosphorylation Report,ġ0: Default Protein Report with non-validated matches, In distributed setups, we recommend keeping a clean copy of PeptideShaker, and distribute it to the different nodes prior to execution. It is recommended to use a single instance of PeptideShakerCLI at a time. Identification parameters can be provided as a file. F) PathSettingsCLI - set the paths to use.E) StirredCLI - export an mzIdentML file from a set of MS identification files produced by search and de novo engines.D) MzidCLI - export an mzIdentML file from a PeptideShaker project.C) FollowUpCLI - export files for follow up analysis from a PeptideShaker project.B) ReportCLI - exports identification results from a PeptideShaker project as text file.A) PeptideShakerCLI - creates a PeptideShaker project.PeptideShaker provides several command line interfaces that can be used to process MS identification files produced by search and de novo engines and output results in various formats. PeptideShakerCLI PeptideShaker Command Line Interface
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