comparison fill_ctd.py @ 13:47982606f542 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

12:da0add7a8abd

    no values of d are overwritten
    """
    for k, v in e.items():
        if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
            mergeDicts(d[k], e[k])
        elif k not in d and not isinstance(e[k], collections.abc.Mapping):
            d[k] = e[k]
        else:
            sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
            sys.exit(1)

    hc_args = json.load(fh, object_hook=_json_object_hook)

# insert the hc_args into the args
mergeDicts(args, hc_args)

if "adv_opts_cond" in args:
    args.update(args["adv_opts_cond"])
    del args["adv_opts_cond"]

# IDMapper has in and spectra:in params, in is used in out as format_source",
# which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
# therefore hardcoded params change the name of spectra:in to spectra:_in
# which is corrected here again

13:47982606f542

    no values of d are overwritten
    """
    for k, v in e.items():
        if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
            mergeDicts(d[k], e[k])
        elif k not in d:
            d[k] = e[k]
        else:
            sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
            sys.exit(1)

    hc_args = json.load(fh, object_hook=_json_object_hook)

# insert the hc_args into the args
mergeDicts(args, hc_args)

# put the contents of the advanced options section into the main dict
if "adv_opts" in args:
    args.update(args["adv_opts"])
    del args["adv_opts"]

# IDMapper has in and spectra:in params, in is used in out as format_source",
# which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
# therefore hardcoded params change the name of spectra:in to spectra:_in
# which is corrected here again