annotate fill_ctd_clargs.py @ 14:856b0f25f4cc draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
author galaxyp
date Wed, 23 Sep 2020 15:01:29 +0000
parents e31fe5424cbe
children 79706b7647c3
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1 #!/usr/bin/env python3
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2 from argparse import ArgumentParser
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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3 from io import StringIO
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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4
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5 from CTDopts.CTDopts import (
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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6 CTDModel,
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7 ModelTypeError,
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8 Parameters
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9 )
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10
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11 if __name__ == "__main__":
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12 # note add_help=False since otherwise arguments starting with -h will
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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13 # trigger an error (despite allow_abbreviate)
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14 parser = ArgumentParser(prog="fill_ctd_clargs",
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 description="fill command line arguments"
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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16 "into a CTD file and write the CTD file to",
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17 add_help=False, allow_abbrev=False)
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18 parser.add_argument("--ctd", dest="ctd", help="input ctd file",
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19 metavar='CTD', default=None, required=True)
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20 args, cliargs = parser.parse_known_args()
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21 # load CTDModel
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22 model = None
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23 try:
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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24 model = CTDModel(from_file=args.ctd)
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25 except ModelTypeError:
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26 pass
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27 try:
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28 model = Parameters(from_file=args.ctd)
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29 except ModelTypeError:
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30 pass
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31 assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd)
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33 # get a dictionary of the ctd arguments where the values of the parameters
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 # given on the command line are overwritten
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35 margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True)
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37 # write the ctd with the values taken from the dictionary
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38 out = StringIO()
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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39 ctd_tree = model.write_ctd(out, margs)
e31fe5424cbe "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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40 print(out.getvalue())