Package eu.isas.peptideshaker.cmd

package eu.isas.peptideshaker.cmd

Command line usage.

Related Packages

Package	Description
eu.isas.peptideshaker	PeptideShaker main calculations and jar wrapper.

Class	Description
CLIExportMethods	This class groups standard methods used by the different command line interfaces.
FollowUpCLI	Command line interface to run follow-up analysis on psdb files.
FollowUpCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
FollowUpCLIParams	Enum class specifying the Command Line Parameters for follow up analysis.
IdentificationParametersCLI	The SearchParametersCLI allows creating search parameters files using command line arguments.
MzidCLI	Command line interface to export mzid files from psdb files.
MzidCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
MzidCLIParams	Enum class specifying the Command Line Parameters for mzid export.
PathSettingsCLI	Allows the user to set the path settings in command line.
PathSettingsCLIInputBean	Parses the command line and retrieves the user input.
PathSettingsCLIParams	Enum of the command line parameters for path setting.
PeptideShakerCLI	A command line interface to run PeptideShaker.
PeptideShakerCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
PeptideShakerCLIParams	Enum class specifying the Command Line Parameters for PeptideShaker.
PeptideShakerIdentificationParametersCLIParams	This class provides the parameters which can be used for the identification parameters cli in PeptideShaker.
ReportCLI	This class performs the command line export of reports in command line.
ReportCLIInputBean	This class is a simple bean wrapping the CLI parameters provided in an Options instance.
ReportCLIParams	This class provides the available reports as command line parameters.
StirredCLI	Command line to manage the modifications.
StirredOptions	Enum class specifying the ModificationsCLI parameters.
StirredOptionsBean	This class parses the parameters from an ModificationsCLI.