#Peptideshaker ptm color zip file#
#Peptideshaker ptm color zip#

#Peptideshaker ptm color 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 '/myFolder/my_search_params.par' identification_files '/myFolder' -spectrum_files '/myFolder'

reference myReference -fasta_file '/myFolder/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 -project_type The type of project (0: psm, 1: peptide, 2: protein).

#Peptideshaker ptm color 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 (.psdb). (*) Not mandatory if these files are part of a zip file input with the identification files. Generated using the GUI or via IdentificationParametersCLI.Įxample: '/myFolder/search_parameters.par'.Īlternatively, IdentificationParametersCLI parameters can be passed directly. id_params (*) The identification parameters file (.par). Example: '/myFolder/file1.mzml,/myFolder/file2.mzml'. 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,Įxample: '/myFolder/file1.omx,/myFolder/file1.mzid,/myFolder/file1.t.xml'. fasta_file (*) The complete path to the FASTA file. Mandatory parameters -reference The reference/name for the project. 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. 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