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comparison fill_ctd.py @ 13:1b03536aa3c9 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:08:22 +0000
parents d063e2fe4ba4
children
comparison
equal deleted inserted replaced
12:9020199dba0a 13:1b03536aa3c9
30 no values of d are overwritten 30 no values of d are overwritten
31 """ 31 """
32 for k, v in e.items(): 32 for k, v in e.items():
33 if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)): 33 if (k in d and isinstance(d[k], dict) and isinstance(e[k], collections.abc.Mapping)):
34 mergeDicts(d[k], e[k]) 34 mergeDicts(d[k], e[k])
35 elif k not in d and not isinstance(e[k], collections.abc.Mapping): 35 elif k not in d:
36 d[k] = e[k] 36 d[k] = e[k]
37 else: 37 else:
38 sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e)) 38 sys.stderr.write("fill_ctd.py: could not merge key %s for %s in %s" % (k, d, e))
39 sys.exit(1) 39 sys.exit(1)
40 40
133 hc_args = json.load(fh, object_hook=_json_object_hook) 133 hc_args = json.load(fh, object_hook=_json_object_hook)
134 134
135 # insert the hc_args into the args 135 # insert the hc_args into the args
136 mergeDicts(args, hc_args) 136 mergeDicts(args, hc_args)
137 137
138 if "adv_opts_cond" in args: 138 # put the contents of the advanced options section into the main dict
139 args.update(args["adv_opts_cond"]) 139 if "adv_opts" in args:
140 del args["adv_opts_cond"] 140 args.update(args["adv_opts"])
141 del args["adv_opts"]
141 142
142 # IDMapper has in and spectra:in params, in is used in out as format_source", 143 # IDMapper has in and spectra:in params, in is used in out as format_source",
143 # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493" 144 # which does not work in Galaxy: https://github.com/galaxyproject/galaxy/pull/9493"
144 # therefore hardcoded params change the name of spectra:in to spectra:_in 145 # therefore hardcoded params change the name of spectra:in to spectra:_in
145 # which is corrected here again 146 # which is corrected here again