The arguments used in the `/main/src/knock_out_simulation.py` file
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This file contains details about the Knockout Simulation arguments.

The default arguments for this script are as follows:

cmd = ' '.join(['python3' , 'knock_out_simulation.py',
              '--context-model', '"{}"'.format(tissueSpecificModelfile),
              '--context-name', '"{}"'.format(context),
              '--disease-name', '"{}"'.format(dis),
              '--disease-up', '"{}"'.format(Disease_Up),
              '--disease-down', '"{}"'.format(Disease_Down),
              '--raw-drug-file', '"{}"'.format(drug_raw_file),
              '--reference-flux-file', '"{}"'.format(ref_flux_file),
              #'--test-all'
               ])
!{cmd}
Argument Required? Default Value Description
--context-model Yes None The context-specific model file, (must be .mat, .xml, or .json
--context-name Yes None Name of context, tissue, cell-type, etc.
--disease-name Yes None The name of the disease
--disease-up yes None The name of the disease up-regulated file
--disease-down Yes None The name of the disease down-regulated file
--raw-drug-file Yes None The name of the raw drug file
--reference-flux-file No None The name of the reference flux file
--test-all No False Test all genes, even ones predicted to have little no effect