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
date Mon, 14 Dec 2020 08:31:14 +0000
parents afc273ea014b
children
line wrap: on
line diff
--- 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())