from clinto import parser
specs = parser.Parser(script_path='/home/chris/Devel/pythomics/pythomics/scripts/proteinInference.py', script_name='Protein Inference')
specs.get_script_description()
{
  'name': 'Protein Inference Script',
  'path': '/home/chris/Devel/pythomics/pythomics/scripts/proteinInference.py'
  'description': '\nThis script will annotate a tab delimited text file with peptides with\ncorresponding proteins present in an annotation file, and can also\nuse this annotation to include iBAQ measures.\n',
  'inputs': {
    'parser_name': [{
      'group': 'optional arguments',
      'nodes': [{
          'choice_limit': None,
          'choices': None,
          'help': 'Threads to run',
          'model': 'IntegerField',
          'name': 'p',
          'param': '-p',
          'required': False,
          'type': 'text',
          'value': 1
        }, {
          'choice_limit': '1',
          'choices': None,
          'help': 'The fasta file to match peptides against.',
          'model': 'FileField',
          'name': 'fasta',
          'param': '-f',
          'required': False,
          'type': 'file',
          'upload': True
        }],
      },
      'group': 'Protein Grouping Options',
      'nodes': [{
          'checked': False,
          'choice_limit': 0,
          'choices': None,
          'help': 'Only group proteins with unique peptides',
          'model': 'BooleanField',
          'name': 'unique_only',
          'param': '--unique-only',
          'required': False,
          'type': 'checkbox'
        }, {
          'checked': False,
          'choice_limit': 0,
          'choices': None,
          'help': 'Write the position of the peptide matches.',
          'model': 'BooleanField',
          'name': 'position',
          'param': '--position',
          'required': False,
          'type': 'checkbox'
        }],
     ]
   },
}