Mercurial > repos > galaxyp > openms_phosphoscoring

comparison fill_ctd.py @ 10:535b554505c6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:08:11 +0000
parents 4c583fde2a28
children 996ca7c1d45e
comparison
equal deleted inserted replaced
9:4c583fde2a28 10:535b554505c6
148 148
149 model = CTDModel(from_file=input_ctd) 149 model = CTDModel(from_file=input_ctd)
150 150
151 # transform values from json that correspond to 151 # transform values from json that correspond to
152 # - old style booleans (string + restrictions) -> transformed to a str 152 # - old style booleans (string + restrictions) -> transformed to a str
153 # - new style booleans that get a string (happens for hidden parameters [-test])
154 # are transformed to a bool
153 # - unrestricted ITEMLIST which are represented as strings 155 # - unrestricted ITEMLIST which are represented as strings
154 # ("=quoted and space separated) in Galaxy -> transform to lists 156 # ("=quoted and space separated) in Galaxy -> transform to lists
155 # - optional data input parameters that have defaults and for which no 157 # - optional data input parameters that have defaults and for which no
156 # value is given -> overwritte with the default 158 # value is given -> overwritte with the default
157 for p in model.get_parameters(): 159 for p in model.get_parameters():
162 try: 164 try:
163 getFromDict(args, p.get_lineage(name_only=True)) 165 getFromDict(args, p.get_lineage(name_only=True))
164 except KeyError: 166 except KeyError:
165 # few tools use dashes in parameters which are automatically replaced 167 # few tools use dashes in parameters which are automatically replaced
166 # by underscores by Galaxy. in these cases the dictionary needs to be 168 # by underscores by Galaxy. in these cases the dictionary needs to be
167 # updated 169 # updated (better: then dash and the underscore variant are in the dict)
168 # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529 170 # TODO might be removed later https://github.com/OpenMS/OpenMS/pull/4529
169 try: 171 try:
170 lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)] 172 lineage = [_.replace("-", "_") for _ in p.get_lineage(name_only=True)]
171 val = getFromDict(args, lineage) 173 val = getFromDict(args, lineage)
172 except KeyError: 174 except KeyError:
173 continue 175 continue
174 else: 176 else:
175 setInDict(args, lineage, val) 177 setInDict(args, p.get_lineage(name_only=True), val)
176 178
177 if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]): 179 if p.type is str and type(p.restrictions) is _Choices and set(p.restrictions.choices) == set(["true", "false"]):
178 v = getFromDict(args, p.get_lineage(name_only=True)) 180 v = getFromDict(args, p.get_lineage(name_only=True))
179 setInDict(args, p.get_lineage(name_only=True), str(v).lower()) 181 setInDict(args, p.get_lineage(name_only=True), str(v).lower())
180 182 elif p.type is bool:
183 v = getFromDict(args, p.get_lineage(name_only=True))
184 if isinstance(v, str):
185 v = (v.lower() == "true")
186 setInDict(args, p.get_lineage(name_only=True), v)
181 elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange): 187 elif p.is_list and (p.restrictions is None or type(p.restrictions) is _NumericRange):
182 v = getFromDict(args, p.get_lineage(name_only=True)) 188 v = getFromDict(args, p.get_lineage(name_only=True))
183 if type(v) is str: 189 if type(v) is str:
184 setInDict(args, p.get_lineage(name_only=True), qstring2list(v)) 190 setInDict(args, p.get_lineage(name_only=True), qstring2list(v))
185 elif p.type is _InFile and not (p.default is None or type(p.default) is _Null): 191 elif p.type is _InFile and not (p.default is None or type(p.default) is _Null):