Class GalaxyToolInterpreter
- java.lang.Object
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- fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
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public class GalaxyToolInterpreter extends Object
This class create an interpreter to tool xml file from Galaxy.- Since:
- 2.0
- Author:
- Sandrine Perrin
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Constructor Summary
Constructors Constructor Description GalaxyToolInterpreter(File file)
Public constructor.GalaxyToolInterpreter(InputStream in, String toolSource)
Public constructor.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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()
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Constructor Detail
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GalaxyToolInterpreter
public GalaxyToolInterpreter(File file) throws EoulsanException, FileNotFoundException
Public constructor.- Parameters:
file
- the Galaxy tool file- Throws:
EoulsanException
- the Eoulsan exceptionFileNotFoundException
- if the file cannot be load
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GalaxyToolInterpreter
public GalaxyToolInterpreter(InputStream in, String toolSource) throws EoulsanException
Public constructor.- Parameters:
in
- the input stream- Throws:
EoulsanException
- the Eoulsan exception
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Method Detail
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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
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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
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getInputs
public Map<String,ToolElement> getInputs()
Gets the inputs.- Returns:
- the inputs
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getOutputs
public Map<String,ToolElement> getOutputs()
Gets the outputs.- Returns:
- the outputs
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getInputDataElements
public Set<DataToolElement> getInputDataElements()
Gets the in data format expected associated with variable found in command line.- Returns:
- the in data format expected
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getOutputDataElements
public Set<DataToolElement> getOutputDataElements()
Gets the out data format expected associated with variable found in command line.- Returns:
- the out data format expected
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getToolInfo
public ToolInfo getToolInfo()
Gets the tool information.- Returns:
- the tool information
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