This converts an assortment of python command line interfaces into a language agnostic build spec for usage in GUI creation.
Here's a basic usage:
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()
{'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': [{'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},
...
{'choice_limit': None,
'choices': None,
'help': 'Where to save the file with motifs. Default: --out file with _motif suffix.',
'model': 'CharField',
'name': 'motif_out',
'param': '--motif-out',
'required': False,
'type': 'text'}]},
{'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'},
{'checked': False,
'choice_limit': 0,
'choices': None,
'help': 'Treat peptides as case-sensitive (ie separate modified peptides)',
'model': 'BooleanField',
'name': 'case_sensitive',
'param': '--case-sensitive',
'required': False,
'type': 'checkbox'}]}],
'name': 'abc',
'path': '/home/chris/Devel/pythomics/pythomics/scripts/proteinInference.py'}