Mercurial > repos > galaxyp > openms_spectrafilterthresholdmower
diff fill_ctd.py @ 10:347d9d613d1b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e9568c650259d95b230d1a243e90f73a19564c2"
author | galaxyp |
---|---|
date | Thu, 24 Sep 2020 09:53:18 +0000 |
parents | e9ec21114394 |
children | 1db101600feb |
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--- a/fill_ctd.py Thu Sep 03 16:20:19 2020 +0000 +++ b/fill_ctd.py Thu Sep 24 09:53:18 2020 +0000 @@ -150,6 +150,8 @@ # 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 @@ -164,7 +166,7 @@ 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 + # 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)] @@ -172,12 +174,16 @@ except KeyError: continue else: - setInDict(args, lineage, val) + 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: