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  • About
    • The spaCy adapter is a python based tool that takes in speech segmentation JSON as input and produces a list of entities. Each entity contains a start, end, type, and label.
  • Source Code
    • galaxy/tools/spacy/spacy.xml
      Tool configuration detailing tool execution, input file, output file, and labeling.
    • galaxy/tools/spacy/spacy_wrapper.py
      Python script to call spaCy tool and conform json to schema
    • galaxy/tools/amp_json_schema/entity_extraction_schema.py
      Set of classes representing the entity extraction schema

  • Dependencies
    • spacy
  • Installation:
            $ pip install spacy

  • Running the tool
    • The tool can be invoked from Galaxy UI as other tools. User needs to supply input data in the form of standardized speech to text output

  • Parameters
    • $input_file: the speech to text output.
    • $json_file: the output json file.


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