Mercurial > repos > iuc > ncbi_entrez_direct_efetch

comparison __efetch_build_options.py @ 0:91efba463050 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
author iuc
date Tue, 22 Mar 2022 22:30:08 +0000
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-1:000000000000 0:91efba463050
1 #!/usr/bin/env python
2
3 # Daniel Blankenberg
4 # Creates the options for tool interface
5
6 # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
7 db_list = '''<DbName>pubmed</DbName>
8 <DbName>protein</DbName>
9 <DbName>nuccore</DbName>
10 <DbName>nucleotide</DbName>
11 <DbName>nucgss</DbName>
12 <DbName>nucest</DbName>
13 <DbName>structure</DbName>
14 <DbName>genome</DbName>
15 <DbName>annotinfo</DbName>
16 <DbName>assembly</DbName>
17 <DbName>bioproject</DbName>
18 <DbName>biosample</DbName>
19 <DbName>blastdbinfo</DbName>
20 <DbName>books</DbName>
21 <DbName>cdd</DbName>
22 <DbName>clinvar</DbName>
23 <DbName>clone</DbName>
24 <DbName>gap</DbName>
25 <DbName>gapplus</DbName>
26 <DbName>grasp</DbName>
27 <DbName>dbvar</DbName>
28 <DbName>gene</DbName>
29 <DbName>gds</DbName>
30 <DbName>geoprofiles</DbName>
31 <DbName>homologene</DbName>
32 <DbName>medgen</DbName>
33 <DbName>mesh</DbName>
34 <DbName>ncbisearch</DbName>
35 <DbName>nlmcatalog</DbName>
36 <DbName>omim</DbName>
37 <DbName>orgtrack</DbName>
38 <DbName>pmc</DbName>
39 <DbName>popset</DbName>
40 <DbName>probe</DbName>
41 <DbName>proteinclusters</DbName>
42 <DbName>pcassay</DbName>
43 <DbName>biosystems</DbName>
44 <DbName>pccompound</DbName>
45 <DbName>pcsubstance</DbName>
46 <DbName>pubmedhealth</DbName>
47 <DbName>seqannot</DbName>
48 <DbName>snp</DbName>
49 <DbName>sra</DbName>
50 <DbName>taxonomy</DbName>
51 <DbName>unigene</DbName>
52 <DbName>gencoll</DbName>
53 <DbName>gtr</DbName>'''.replace("<DbName>", "").replace("</DbName>", "").split("\n")
54
55
56 help = ''' (all)
57 docsum DocumentSummarySet XML
58 docsum json DocumentSummarySet JSON
59 full Same as native except for mesh
60 uid Unique Identifier List
61 url Entrez URL
62 xml Same as -format full -mode xml
63
64 bioproject
65 native BioProject Report
66 native xml RecordSet XML
67
68 biosample
69 native BioSample Report
70 native xml BioSampleSet XML
71
72 biosystems
73 native xml Sys-set XML
74
75 gds
76 native xml RecordSet XML
77 summary Summary
78
79 gene
80 gene_table Gene Table
81 native Gene Report
82 native asn.1 Entrezgene ASN.1
83 native xml Entrezgene-Set XML
84 tabular Tabular Report
85
86 homologene
87 alignmentscores Alignment Scores
88 fasta FASTA
89 homologene Homologene Report
90 native Homologene List
91 native asn.1 HG-Entry ASN.1
92 native xml Entrez-Homologene-Set XML
93
94 mesh
95 full Full Record
96 native MeSH Report
97 native xml RecordSet XML
98
99 nlmcatalog
100 native Full Record
101 native xml NLMCatalogRecordSet XML
102
103 pmc
104 medline MEDLINE
105 native xml pmc-articleset XML
106
107 pubmed
108 abstract Abstract
109 medline MEDLINE
110 native asn.1 Pubmed-entry ASN.1
111 native xml PubmedArticleSet XML
112
113 (sequences)
114 acc Accession Number
115 est EST Report
116 fasta FASTA
117 fasta xml TinySeq XML
118 fasta_cds_aa FASTA of CDS Products
119 fasta_cds_na FASTA of Coding Regions
120 ft Feature Table
121 gb GenBank Flatfile
122 gb xml GBSet XML
123 gbc xml INSDSet XML
124 gbwithparts GenBank with Contig Sequences
125 gene_fasta FASTA of Gene
126 gp GenPept Flatfile
127 gp xml GBSet XML
128 gpc xml INSDSet XML
129 gss GSS Report
130 ipg Identical Protein Report
131 ipg xml IPGReportSet XML
132 native text Seq-entry ASN.1
133 native xml Bioseq-set XML
134 seqid Seq-id ASN.1
135
136 snp
137 chr Chromosome Report
138 docset Summary
139 fasta FASTA
140 flt Flat File
141 native asn.1 Rs ASN.1
142 native xml ExchangeSet XML
143 rsr RS Cluster Report
144 ssexemplar SS Exemplar List
145
146 sra
147 native xml EXPERIMENT_PACKAGE_SET XML
148 runinfo xml SraRunInfo XML
149
150 structure
151 mmdb Ncbi-mime-asn1 strucseq ASN.1
152 native MMDB Report
153 native xml RecordSet XML
154
155 taxonomy
156 native Taxonomy List
157 native xml TaxaSet XML'''.split("\n")
158
159 db = {}
160 name = None
161 all = "(all)"
162 for line in help:
163 if line.strip() and line[2] != ' ':
164 name = line.strip()
165 db[name] = {}
166 elif line.strip():
167 format = line[0:len(" docsum ")].strip()
168 mode = line[len(" docsum "):len(" docsum json ")].strip()
169 if format not in db[name]:
170 db[name][format] = []
171 db[name][format].append(mode)
172
173 for name in db_list:
174 if name not in db:
175 db[name] = {}
176
177 db["sequences"] = db["(sequences)"]
178 del db["(sequences)"]
179
180 print('<conditional name="db">')
181 print(' <param name="db" type="select" label="Database" argument="-db">')
182 for name in sorted(db.keys()):
183 if name == all:
184 continue
185 print(' <option value="%s">%s</option>' % (name, name))
186 print(' <option value="">Manual Entry</option>')
187 print(' </param>')
188
189 for name in sorted(db.keys()):
190 if name == all:
191 continue
192 my_dict = db[all].copy()
193
194 for format, modes in db[name].items():
195 if format in my_dict:
196 for mode in modes:
197 if mode not in my_dict[format]:
198 my_dict[format].append(mode)
199 else:
200 my_dict[format] = modes
201 if "" not in my_dict:
202 my_dict[""] = [""]
203 print(' <when value="%s">' % name)
204 print(' <conditional name="format">')
205 print(' <param name="format" type="select" label="Format" argument="-format">')
206 for format in sorted(my_dict.keys()):
207 print(' <option value="%s">%s</option>' % (format, format or "None"))
208 print(' </param>')
209 for format in sorted(my_dict.keys()):
210 print(' <when value="%s">' % format)
211 print(' <param name="mode" type="select" label="Mode" argument="-mode">')
212 if "" not in my_dict[format]:
213 my_dict[format].append("")
214 for mode in sorted(my_dict[format]):
215 print(' <option value="%s">%s</option>' % (mode, mode or "None"))
216 print(' </param>')
217 print(' </when>')
218 print(' </conditional>')
219 print(' </when>')
220 print(' <when value="">')
221 print(' <param name="db_manual" type="text" label="Database" argument="-db"/>')
222 print(' <param name="format" type="text" label="Format" argument="-format"/>')
223 print(' <param name="mode" type="text" label="Mode" argument="-mode"/>')
224 print(' </when>')
225 print('</conditional>')