
Basic usage with a JSON input parameter file

  python3 src/tcell_mhcii.py -j <input_json_file> [-o] <output_prefix> [-f] <output_format>

  * output_format: tsv (default), json

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| * Show basic usage information                                                                                        |
| python3 src/tcell_mhcii.py -h                                                                                          |
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| * List available methods and versions                                                                                 |
| python3 src/tcell_mhcii.py -v                                                                                          |
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| * Run a binding prediction, specifying input parameters via a JSON file                                               |
| python3 src/tcell_mhcii.py  -j [input_json_file]                                                                       |
| Example: python3 src/tcell_mhcii.py  -j examples/binding.json                                                          |
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IEDB internal usage and specialized use cases
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| * Split a large job into smaller units                                                                                |
| python3 src/tcell_mhcii.py -j [input_json_file] --split --split-dir=[atomic_units_json_file_dir]                       |
| Example: python3 src/tcell_mhcii.py -j examples/input_sequence_text.json --split --split-dir=job1/parameter_units           |
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| Among other outputs, a 'job_descriptions.json' file will be created that will specify the commands to use for each    |
| individual job.  A future release of NG Tools may include code for managing these jobs.                               |
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