Package fr.ens.biologie.genomique.eoulsan.galaxytools

Class GalaxyToolInterpreter

java.lang.Object

fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter

public class GalaxyToolInterpreter
extends Object

This class create an interpreter to tool xml file from Galaxy.

Since:

2.0

Author:

Sandrine Perrin

Constructor Summary

Constructors

Constructor	Description
GalaxyToolInterpreter(File file)	Public constructor.
GalaxyToolInterpreter(InputStream in, String toolSource)	Public constructor.
GalaxyToolInterpreter(Path file)	Public constructor.

Method Summary

Modifier and Type	Method	Description
void	configure(Set<Parameter> parameters)	Parse tool file to extract useful data to run tool.
ToolExecutorResult	execute(TaskContext context)	Convert command tag from tool file in string, variable are replace by value.
Set<DataToolElement>	getInputDataElements()	Gets the in data format expected associated with variable found in command line.
Map<String,ToolElement>	getInputs()	Gets the inputs.
Set<DataToolElement>	getOutputDataElements()	Gets the out data format expected associated with variable found in command line.
Map<String,ToolElement>	getOutputs()	Gets the outputs.
ToolInfo	getToolInfo()	Gets the tool information.
static String	removeNamespace(String variableName)	Remove the namespace from the name of a variable.
String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

GalaxyToolInterpreter

public GalaxyToolInterpreter(File file)
                      throws EoulsanException,
IOException

Public constructor.

Parameters:

file - the Galaxy tool file

Throws:

EoulsanException - the Eoulsan exception

IOException - if the file cannot be load

GalaxyToolInterpreter

public GalaxyToolInterpreter(Path file)
                      throws EoulsanException,
IOException

Public constructor.

Parameters:

file - the Galaxy tool file

Throws:

EoulsanException - the Eoulsan exception

IOException - if the file cannot be load

GalaxyToolInterpreter

public GalaxyToolInterpreter(InputStream in,
 String toolSource)
                      throws EoulsanException

Public constructor.

Parameters:

in - the input stream

toolSource - tool source

Throws:

EoulsanException - the Eoulsan exception

Method Details

configure

public void configure(Set<Parameter> parameters)
               throws EoulsanException

Parse tool file to extract useful data to run tool.

Parameters:

parameters - the set step parameters

Throws:

EoulsanException - if an data missing

execute

public ToolExecutorResult execute(TaskContext context)
                           throws EoulsanException

Convert command tag from tool file in string, variable are replace by value.

Parameters:

context - the context

Returns:

the string

Throws:

EoulsanException - the Eoulsan exception

getInputs

public Map<String,ToolElement> getInputs()

Gets the inputs.

Returns:

the inputs

getOutputs

public Map<String,ToolElement> getOutputs()

Gets the outputs.

Returns:

the outputs

getInputDataElements

public Set<DataToolElement> getInputDataElements()

Gets the in data format expected associated with variable found in command line.

Returns:

the in data format expected

getOutputDataElements

public Set<DataToolElement> getOutputDataElements()

Gets the out data format expected associated with variable found in command line.

Returns:

the out data format expected

getToolInfo

public ToolInfo getToolInfo()

Gets the tool information.

Returns:

the tool information

toString

public String toString()

Overrides:

toString in class Object

removeNamespace

public static String removeNamespace(String variableName)

Remove the namespace from the name of a variable.

Parameters:

variableName - variable name

Returns:

the variable name without the namespace