Package fr.ens.biologie.genomique.eoulsan.modules

Class GalaxyToolModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule

All Implemented Interfaces:

Module

public class GalaxyToolModule
extends AbstractModule

The Class GalaxyToolStep.

Since:

2.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
GalaxyToolModule(InputStream toolXMLis)	Constructor.
GalaxyToolModule(InputStream in, String source)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
OutputPorts	getOutputPorts()	Get the output data format.
Set<Requirement>	getRequirements()	Get the requirements of the module.
String	getSource()	Get the source the Galaxy tool.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getChecker, getDescription, getParallelizationMode, getRequiredEoulsanVersion

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GalaxyToolModule

public GalaxyToolModule(InputStream toolXMLis)
                 throws EoulsanException

Constructor.

Parameters:

toolXMLis - the input stream on tool xml file

Throws:

EoulsanException - the Eoulsan exception

GalaxyToolModule

public GalaxyToolModule(InputStream in,
                        String source)
                 throws EoulsanException

Constructor.

Parameters:

in - the input stream for XML tool file

source - source of the Galaxy tool

Throws:

EoulsanException - the Eoulsan exception

Method Detail

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getVersion

public fr.ens.biologie.genomique.kenetre.util.Version getVersion()

Description copied from interface: Module

Get version of the Module.

Returns:

a Version object with the version of the Module

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

a set with DataFormat or null if the module does not any need input format

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractModule

Returns:

an set with DataFormat or null if the module does not produce any output data

getRequirements

public Set<Requirement> getRequirements()

Description copied from interface: Module

Get the requirements of the module.

Specified by:

getRequirements in interface Module

Overrides:

getRequirements in class AbstractModule

Returns:

a set with the requirements of the module

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task

getSource

public String getSource()

Get the source the Galaxy tool.

Returns:

the source of the Galaxy tool