comparison fill_ctd.py @ 10:8a45fd5a608a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

9:f874f2998576

model = CTDModel(from_file=input_ctd)

# transform values from json that correspond to
# - old style booleans (string + restrictions) -> transformed to a str
# - unrestricted ITEMLIST which are represented as strings
#   ("=quoted and space separated) in Galaxy -> transform to lists
# - optional data input parameters that have defaults and for which no
#   value is given -> overwritte with the default
for p in model.get_parameters():

    try:
        getFromDict(args, p.get_lineage(name_only=True))
    except KeyError:
        # few tools use dashes in parameters which are automatically replaced
        # by underscores by Galaxy. in these cases the dictionary needs to be
        # updated
        # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
        try:
            lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)]
            val = getFromDict(args, lineage)
        except KeyError:
            continue
        else:
            setInDict(args, lineage, val)

    if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]):
        v = getFromDict(args, p.get_lineage(name_only=True))
        setInDict(args, p.get_lineage(name_only=True), str(v).lower())

    elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange):
        v = getFromDict(args, p.get_lineage(name_only=True))
        if type(v) is str:
            setInDict(args, p.get_lineage(name_only=True), qstring2list(v))
    elif p.type is _InFile and not (p.default is None or type(p.default) is _Null):

10:8a45fd5a608a

model = CTDModel(from_file=input_ctd)

# transform values from json that correspond to
# - old style booleans (string + restrictions) -> transformed to a str
# - new style booleans that get a string (happens for hidden parameters [-test])
#   are transformed to a bool
# - unrestricted ITEMLIST which are represented as strings
#   ("=quoted and space separated) in Galaxy -> transform to lists
# - optional data input parameters that have defaults and for which no
#   value is given -> overwritte with the default
for p in model.get_parameters():

    try:
        getFromDict(args, p.get_lineage(name_only=True))
    except KeyError:
        # few tools use dashes in parameters which are automatically replaced
        # by underscores by Galaxy. in these cases the dictionary needs to be
        # updated (better: then dash and the underscore variant are in the dict)
        # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
        try:
            lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)]
            val = getFromDict(args, lineage)
        except KeyError:
            continue
        else:
            setInDict(args, p.get_lineage(name_only=True), val)

    if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]):
        v = getFromDict(args, p.get_lineage(name_only=True))
        setInDict(args, p.get_lineage(name_only=True), str(v).lower())
    elif p.type is bool:
        v = getFromDict(args, p.get_lineage(name_only=True))
        if isinstance(v, str):
            v = (v.lower() == "true")
            setInDict(args, p.get_lineage(name_only=True), v)
    elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange):
        v = getFromDict(args, p.get_lineage(name_only=True))
        if type(v) is str:
            setInDict(args, p.get_lineage(name_only=True), qstring2list(v))
    elif p.type is _InFile and not (p.default is None or type(p.default) is _Null):