Class GalaxyToolInterpreter


  • public class GalaxyToolInterpreter
    extends Object
    This class create an interpreter to tool xml file from Galaxy.
    Since:
    2.0
    Author:
    Sandrine Perrin
    • Method Detail

      • 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
      • 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
      • 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