Mercurial > repos > galaxyp > openms_msgfplusadapter
diff fill_ctd_clargs.py @ 20:088df56a7fac draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author | galaxyp |
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date | Mon, 14 Dec 2020 08:31:14 +0000 |
parents | afc273ea014b |
children |
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--- a/fill_ctd_clargs.py Fri Nov 06 18:21:13 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -#!/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())