Mercurial > repos > galaxyp > openms_openpepxllf
view fill_ctd_clargs.py @ 6:e574d3f268f6 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
---|---|
date | Tue, 13 Oct 2020 20:10:48 +0000 |
parents | 04168c0bdfa7 |
children | 8bfa9d787dc7 |
line wrap: on
line source
#!/usr/bin/env python3 from argparse import ArgumentParser from io import StringIO from CTDopts.CTDopts import ( CTDModel, ModelTypeError, Parameters ) if __name__ == "__main__": # note add_help=False since otherwise arguments starting with -h will # trigger an error (despite allow_abbreviate) parser = ArgumentParser(prog="fill_ctd_clargs", description="fill command line arguments" "into a CTD file and write the CTD file to", add_help=False, allow_abbrev=False) parser.add_argument("--ctd", dest="ctd", help="input ctd file", metavar='CTD', default=None, required=True) args, cliargs = parser.parse_known_args() # load CTDModel model = None try: model = CTDModel(from_file=args.ctd) except ModelTypeError: pass try: model = Parameters(from_file=args.ctd) except ModelTypeError: pass assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd) # get a dictionary of the ctd arguments where the values of the parameters # given on the command line are overwritten margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True) # write the ctd with the values taken from the dictionary out = StringIO() ctd_tree = model.write_ctd(out, margs) print(out.getvalue())