ReportCLI example where X, Y and Z have to be replaced by the actual version of PeptideShaker: java -cp PeptideShaker-X.Y.Z.jar eu. To add custom reports see Export > Identification Features > Reports in PeptideShaker. 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. Optional report options -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, out_reports Output folder for report files.
Peptideshaker compomics zip#
Mandatory parameters -in PeptideShaker project (.psdb or zip file) Standard command line java -cp PeptideShaker-X.Y.Z.jar eu.
When used the command should of course be a single line. Note that for readability the command is here split over multiple lines. id_params "C:\my folder\my_search_params.par" identification_files "C:\my folder" -spectrum_files "C:\my folder" reference myReference -fasta_file "C:\my folder\my_data.fasta" PeptideShakerCLI example where X, Y and Z have to be replaced by the actual version of PeptideShaker and my folder by the folder containing the desired files: java -cp PeptideShaker-X.Y.Z.jar eu. gui Use a dialog to display the progress (1: true, 0: false, default is '0'). Defaults to the number of available CPUs. Optional processing parameters -threads The number of threads to use.
Peptideshaker compomics zip file#
output_mgf When using zipped output, exports mgf file(s) out of the zip file zip Exports the entire project as a zip file in the file specified. Optional output parameters -out PeptideShaker output file (.cpsx). (*) 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. 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. PeptideShakerCLI PeptideShaker Command Line Interface
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