It is recommended to use a single instance of PeptideShakerCLI 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 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. 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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