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PeptideShakerCLI
The PeptideShaker command line interface can be used to process identification files and output identification results in various formats.
There are six main sections to this page:
- A) PeptideShakerCLI - data processing
- B) ReportCLI - identification results exports
- C) FollowUpCLI - export for follow up analysis
- D) MzidCLI - export as mzIdentML
- E) PathSettingsCLI - set the paths to use
- E) General - general command line help
Note that ReportCLI, FollowUpCLI, MzidCLI and PathSettingsCLI options can also be appended to PeptideShakerCLI command lines.
All command line options have the same overall structure and only differ in the features and parameters available.
The recommended way to generate an identification parameters file for use in PeptideShakerCLI, is via the SearchGUI graphical user interface. But the file can also be created using the IdentificationParametersCLI.
Standard command line
java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI [parameters]Mandatory parameters
-experiment Specifies the experiment name.
-sample Specifies the sample name.
-replicate The replicate number.
-identification_files Identification files (X!Tandem .t.xml, mzIdentML .mzid, MS Amanda .cvs,
OMSSAgo .omx, Mascot .dat files, Tide .txt, Comet .pep.xml or .zip)
in a comma separated list or an entire folder.
Example: "c:\file1.omx, c:\file1.dat, c:\file1.t.xml".
-out PeptideShaker output file (.cpsx). If the file already exists
it will be silently overwritten.
Example: "c:\ps_output.cpsx".
-spectrum_files (*) The spectrum files (mgf format) in a comma
separated list or an entire folder.
Example: "c:\file1.mgf, c:\file2.mgf".
-id_params (*) The identification parameters file (.par).
Generated using SeachGUI or via IdentificationParametersCLI.
This file is automatically saved by SearchGUI along with the
identification files.
Example: "c:\search_parameters.par".
(*) Not mandatory if these files are part of a zip file input with the identification files.
Optional gene annotation parameter
-species The species to use for the gene annotation, e.g., 'Homo sapiens'.
Supported species are listed in the GUI.
-species_type The species type to use for the gene annotation, e.g., 'Vertebrates' or 'Plants'.
Supported species types are listed in the GUI.
-species_update Check for new species information in Ensembl and update if possible.
(1: true, 0: false, default is '0').
Optional validation parameters
-protein_FDR FDR at the protein level in percent
(default 1% FDR: '1').
-peptide_FDR FDR at the peptide level in percent
(default 1% FDR: '1').
-psm_FDR FDR at the PSM level in percent (default 1%
FDR: '1').
-protein_fraction_mw_confidence
Minimum confidence required for a protein in
the fraction MW plot (default 95%: '95.0').
Optional PTM localization scoring parameters
-ptm_score The PTM probabilistic score to use for PTM localization
(0: A-score, 1: PhosphoRS, 2: None, default is '1').
-ptm_threshold The threshold to use for the PTM scores. If none set,
an automatic threshold will be used.
-score_neutral_losses Include neutral losses of mass different from the PTM
in spectrum annotation of the PTM score
(1: true, 0: false, default is '0').
Optional filtering parameters
-min_peptide_length Minimim peptide length filter (default is '4').
-max_peptide_length Maximum peptide length filter (default is '30').
-max_precursor_error Maximum precursor error filter (no filter is used by default).
See also max_precursor_error_type.
-max_precursor_error_type Maximum precursor error type (0: ppm, 1: Da, default is '0').
See also max_precursor_error.
-exclude_unknown_ptms Exclude unknown PTMs (1: true, 0: false, default is '1').
Optional export parameters
-zip Exports the entire project as a zip file in the file specified.
Optional processing parameters
-threads The number of threads to use. Defaults to the number of available CPUs.
-gui Use a dialog to display the progress (1: true, 0: false, default is '0').
PeptideShakerCLI Example
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.isas.peptideshaker.cmd.PeptideShakerCLI
-experiment myExperiment -sample mySample -replicate 1
-identification_files "C:\my folder" -spectrum_files "C:\my folder"
-id_params "C:\my folder\my_search_params.parameters"
-out "C:\my folder\myCpsFile.cpsx"Note that for readability the command is here split over multiple lines. When used the command should of course be a single line.
Standard command line
java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.ReportCLI [parameters]Mandatory parameters
-in PeptideShaker project (.cpsx file)
-out_reports Output folder for report files. (Existing files will be overwritten.)
Optional report options
-reports Comma separated list of types of report to export.
0: Certificate of Analysis,
1: Default Hierarchical Report,
2: Default PSM Phosphorylation Report,
3: Default PSM Report,
4: Default Peptide Phosphorylation Report,
5: Default Peptide Report,
6: Default Protein Phosphorylation Report,
7: Default Protein Report,
8-n: Your own custom reports.
-documentation Comma separated list of types of report documentation to export.
0: Certificate of Analysis,
1: Default Hierarchical Report,
2: Default PSM Phosphorylation Report,
3: Default PSM Report,
4: Default Peptide Phosphorylation Report,
5: Default Peptide Report,
6: Default Protein Phosphorylation Report,
7: Default Protein Report,
8-n: Your own custom reports.
To add custom reports see Export > Identification Features > Reports in PeptideShaker.
ReportCLI Example
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.isas.peptideshaker.cmd.ReportCLI
-in "C:\my folder\myCpsFile.cpsx" -out_reports "C:\my folder" -reports "0, 3"Standard command line
java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.FollowUpCLI [parameters]Mandatory parameters
-in PeptideShaker project (.cpsx file)
Optional recalibration parameters
-recalibration_folder Output folder for the recalibrated files. (Existing files will be overwritten.)
-recalibration_mode Recalibration type.
0: precursor and fragment ions (default),
1: precursor only,
2: fragment ions only.
Optional spectrum export parameters
-spectrum_folder Output folder for the spectra. (Existing files will be overwritten.)
-psm_type Type of PSMs.
0: Spectra of Non-Validated PSMs (default),
1: Spectra of Non-Validated Peptides,
2: Spectra of Non-Validated Proteins,
3: Spectra of Validated PSMs,
4: Spectra of Validated PSMs of Validated Peptides,
5: Spectra of validated PSMs of Validated Peptides of Validated Proteins.
Optional Progenesis export parameters
-progenesis_file Output file for identification results in Progenesis LC-MS compatible format.
(Existing files will be overwritten.)
-progenesis_type Type of hits to export to Progenesis.
0: Validated PSMs of Validated Peptides of Validated Proteins.
1: Validated PSMs of Validated Peptides,
2: Validated PSMs,
3: Validated PSMs containing confidently localized PTMs.
-progenesis_ptms Comma separated list of PTMs to include in reports of Type 3.
Optional protein accessions export parameters
-accessions_file Output file to export the protein accessions in text format.
(Existing files will be overwritten.)
-accessions_type When exporting accessions, select a category of proteins.
0: Main Accession of Validated Protein Groups (default),
1: All Accessions of Validated Protein Groups,
2: Non-Validated Accessions.
Optional FASTA export parameters
-fasta_file File where to export the protein details in fasta format.
(Existing files will be overwritten.)
-fasta_type When exporting protein details, select a category of proteins.
0: Main Accession of Validated Protein Groups (default),
1: All Accessions of Validated Protein Groups,
2: Non-Validated Accessions.
Optional inclusion list generation parameters
-inclusion_list_file Output file for an inclusion list of validated hits.
(Existing files will be overwritten.)
-inclusion_list_format Format for the inclusion list.
0: Thermo (default),
1: ABI,
2: Bruker,
3: MassLynx.
-inclusion_list_peptide_filters
Peptide filters to be used for the inclusion list export (comma separated).
0: Miscleaved Peptides,
1: Reactive Peptides,
2: Degenerated Peptides.
-inclusion_list_protein_filters
Protein inference filters to be used for the inclusion list export (comma separated).
1: Related Proteins,
2: Related and Unrelated Proteins,
3: Unrelated Proteins.
-inclusion_list_rt_window Retention time window for the inclusion list export (in seconds).
FollowUpCLI Example
FollowUpCLI 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.isas.peptideshaker.cmd.FollowUpCLI -in "C:\my folder\myCpsFile.cpsx" -spectrum_folder "C:\my folder" -psm_type 0Standard command line
java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.MzidCLI [parameters]Mandatory parameters
-in PeptideShaker project (.cpsx file)
-output_file Output file.
-contact_first_name Contact first name.
-contact_last_name Contact last name.
-contact_email Contact e-mail.
-contact_address Contact address.
-organization_name Organization name.
-organization_email Organization e-mail.
-organization_address Organization address.
Optional parameters:
-contact_url Contact URL.
-organization_url Organization URL.
Standard command line
java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PathSettingsCLI [parameters]Generic temporary folder
-temp_folder A folder for temporary file storage. Use only if
you encounter problems with the default configuration.
Specific path setting
-peptideshaker_matches_directory
Folder where identification matches are temporarily
saved to reduce the memory footprint.
-peptideshaker_user_preferences
Folder containing the PeptideShaker user preferences file.
-peptideshaker_exports Folder containing the user custom exports file.
-utilities_user_preferences
Folder containing the compomics utilities user preferences file.
-ptm_configuration Folder containing the PTM user preferences file.
-fasta_indexes Folder containing the indexes of the protein sequences databases.
-gene_mapping Folder containing the gene mapping files.
-pride_annotation Folder containing the PRIDE annotation preferences.
Comma Separated Lists
When using comma separated lists as input please pay attention to the quotes required. Surround the full content of the option in quotes and not the individual items:
-spectrum_files "C:\..\file_1.mgf, C:\..\file_2.mgf"Absolute Paths
In general it is recommended to use absolute paths.
Memory Settings
Remember that big datasets require more than the default memory provided to the Java virtual machine, so for larger dataset please increase the maximum memory setting. Example, for a maximum of 2GB of memory:
java -Xmx2048M -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI [parameters]See also: JavaTroubleShooting.
Opening PeptideShaker Projects
To open a PeptideShaker project (cps file or zipped cps file) from the command line (for display in PeptideShaker) use the following command:
java -jar PeptideShaker-X.Y.Z.jar -cps "C:\my folder\myCpsFile.cpsx"To open a zipped PeptideShaker project via a URL from the command line (for display in PeptideShaker) use the following command:
java -jar PeptideShaker-X.Y.Z.jar -zipUrl "http://my_url/PS.zip" -zipUrlFolder C:\my folder\"Help
If you experience any problems with the command line or have any suggestion please contact us via the PeptideShaker mailing list or set up an issue using the issue tracking system.