Mercurial > repos > iuc > ncbi_eutils_efetch

annotate __efetch_build_options.py @ 8:b151cd22921f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:42:47 +0000
parents 2ff5369b4b51
children
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1 #!/usr/bin/env python
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2 # Daniel Blankenberg
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3 # Creates the options for tool interface
6
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4 from __future__ import print_function
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5
3
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6 import re
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8 # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
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9 db_list = '''
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10 <DbName>annotinfo</DbName>
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11 <DbName>assembly</DbName>
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12 <DbName>bioproject</DbName>
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13 <DbName>biosample</DbName>
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14 <DbName>biosystems</DbName>
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15 <DbName>blastdbinfo</DbName>
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16 <DbName>books</DbName>
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17 <DbName>cdd</DbName>
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18 <DbName>clinvar</DbName>
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19 <DbName>clone</DbName>
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20 <DbName>dbvar</DbName>
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21 <DbName>gap</DbName>
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22 <DbName>gapplus</DbName>
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23 <DbName>gds</DbName>
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24 <DbName>gencoll</DbName>
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25 <DbName>gene</DbName>
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26 <DbName>genome</DbName>
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27 <DbName>geoprofiles</DbName>
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28 <DbName>grasp</DbName>
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29 <DbName>gtr</DbName>
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30 <DbName>homologene</DbName>
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31 <DbName>medgen</DbName>
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32 <DbName>mesh</DbName>
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33 <DbName>ncbisearch</DbName>
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34 <DbName>nlmcatalog</DbName>
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35 <DbName>nuccore</DbName>
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36 <DbName>nucest</DbName>
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37 <DbName>nucgss</DbName>
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38 <DbName>nucleotide</DbName>
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39 <DbName>omim</DbName>
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40 <DbName>orgtrack</DbName>
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41 <DbName>pcassay</DbName>
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42 <DbName>pccompound</DbName>
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43 <DbName>pcsubstance</DbName>
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44 <DbName>pmc</DbName>
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45 <DbName>popset</DbName>
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46 <DbName>probe</DbName>
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47 <DbName>protein</DbName>
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48 <DbName>proteinclusters</DbName>
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49 <DbName>pubmed</DbName>
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50 <DbName>pubmedhealth</DbName>
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51 <DbName>seqannot</DbName>
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52 <DbName>snp</DbName>
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53 <DbName>sra</DbName>
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54 <DbName>structure</DbName>
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55 <DbName>taxonomy</DbName>
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b151cd22921f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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56 <DbName>unigene</DbName>'''.replace("<DbName>", "").replace("</DbName>", "").split("\n")
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59 help = ''' (all)
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60 docsum xml Document Summary
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61 docsum json Document Summary
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62 full text Full Document
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63 uilist xml Unique Identifier List
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64 uilist text Unique Identifier List
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65 full xml Full Document
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67 bioproject
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68 native BioProject Report
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69 native xml RecordSet
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71 biosample
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72 native BioSample Report
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73 native xml BioSampleSet
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75 biosystems
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76 native xml Sys-set
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78 gds
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79 native xml RecordSet
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80 summary text Summary
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82 gene
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83 gene_table xml Gene Table
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84 native text Gene Report
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85 native asn.1 Entrezgene
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86 native xml Entrezgene-Set
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87 tabular tabular Tabular Report
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89 homologene
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90 alignmentscores text Alignment Scores
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
91 fasta fasta FASTA
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
92 homologene text Homologene Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
93 native text Homologene List
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
94 native asn.1 HG-Entry
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
95 native xml Entrez-Homologene-Set
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
96
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
97 mesh
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
98 full text Full Record
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
99 native text MeSH Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
100 native xml RecordSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
101
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
102 nlmcatalog
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
103 native text Full Record
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
104 native xml NLMCatalogRecordSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
105
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
106 pmc
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
107 medline text MEDLINE
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
108 native xml pmc-articleset
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
109
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
110 pubmed
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
111 abstract xml Abstract
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
112 medline text MEDLINE
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
113 native asn.1 Pubmed-entry
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
114 native xml PubmedArticleSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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115
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
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116 (sequences)
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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117 acc text Accession Number
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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118 est xml EST Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
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119 fasta fasta FASTA
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
120 fasta xml TinySeq
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
121 fasta_cds_aa fasta CDS Products
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
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122 fasta_cds_na fasta Coding Regions
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
123 ft text Feature Table
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
124 gb text GenBank Flatfile
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
125 gb xml GBSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
126 gbc xml INSDSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
127 gbwithparts text GenBank with Contig Sequences
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
128 gene_fasta fasta FASTA of Gene
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
129 gp text GenPept Flatfile
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
130 gp xml GBSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
131 gpc xml INSDSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
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132 gss text GSS Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
133 ipg text Identical Protein Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
134 ipg xml IPGReportSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
135 native text Seq-entry
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
136 native xml Bioseq-set
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
137 seqid asn.1 Seq-id
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
138
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
139 snp
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
140 chr text Chromosome Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
141 docset text Summary
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
142 fasta fasta FASTA
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
143 flt text Flat File
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
144 native asn.1 Rs
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
145 native xml ExchangeSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
146 rsr tabular RS Cluster Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
147 ssexemplar text SS Exemplar List
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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148
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
149 sra
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
150 native xml EXPERIMENT_PACKAGE_SET
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
151 runinfo xml SraRunInfo
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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152
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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153 structure
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
154 mmdb asn.1 Ncbi-mime-asn1 strucseq
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
155 native text MMDB Report
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
156 native xml RecordSet
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
157
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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158 taxonomy
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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159 native text Taxonomy List
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
160 native xml TaxaSet'''.split("\n")
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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161
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iuc
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162
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
163 db = {}
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
164 for db_name in db_list:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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165 db[db_name] = []
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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166
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
167 section = None
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
168 for line in help:
6
2ff5369b4b51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 5
diff changeset
169 line = re.split(r'\s{2,}', line.strip())
3
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
170 # Ignore empties
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
171 if len(line) == 0:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
172 continue
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
173 # Section headers have one item
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
174 elif len(line) == 1:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
175 section = line[0]
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
176 db[section] = []
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
177 # Format lines have 2+
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
178 elif len(line) == 2:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
179 parent_format = line[0]
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
180 description = line[1]
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
181
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
182 if parent_format not in db[section]:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
183 db[section].append((parent_format, None, description))
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
184 elif len(line) == 3:
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iuc
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diff changeset
185 parent_format = line[0]
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iuc
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186 format_modifier = line[1]
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iuc
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187 description = line[2]
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188
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iuc
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189 if parent_format not in db[section]:
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iuc
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190 db[section].append((parent_format, format_modifier, description))
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191
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192
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iuc
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193 all_formats = db['(all)']
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194 del db['(all)']
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195 sequences_formats = db['(sequences)']
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196 del db['(sequences)']
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197 del db['']
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198
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199 for key in db:
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200 db[key] += all_formats
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201
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iuc
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202 for key in ('nuccore', 'nucest', 'nucgss', 'nucleotide'):
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iuc
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203 db[key] += sequences_formats
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204
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iuc
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205 MACRO_TPL = '''
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iuc
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206
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iuc
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207 '''
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208
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iuc
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209 WHEN_TPL = ''' <when value="{format}">
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iuc
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210 <param name="output_format" type="select" label="Output Format">
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iuc
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211 {format_options}
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212 </param>
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iuc
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213 </when>'''
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214
5
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iuc
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215 FORMAT_OPTION_TPL = '''<option value="{name_type}">{name_type_human}</option>'''
3
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216
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iuc
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217 format_names = {}
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218
6
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219 print(''' <xml name="db">
3
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220 <conditional name="db">
6
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iuc
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221 <expand macro="dbselect" />''')
3
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iuc
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222 for key in sorted(db):
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iuc
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223 format_options = []
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224
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iuc
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diff changeset
225 for (parent_format, format_modifier, description) in sorted(db[key]):
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iuc
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226 name_human = description
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iuc
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diff changeset
227 if format_modifier:
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iuc
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228 name_human += ' (%s)' % format_modifier
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iuc
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229 format_string = '%s-%s' % (parent_format, format_modifier)
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230
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iuc
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diff changeset
231 format_options.append(FORMAT_OPTION_TPL.format(
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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232 name_type=format_string,
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iuc
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233 name_type_human=name_human,
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234 ))
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235
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iuc
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236 format_names[format_string] = format_modifier
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237
6
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diff changeset
238 print(WHEN_TPL.format(
3
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iuc
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diff changeset
239 format=key,
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240 format_options='\n '.join(format_options)
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diff changeset
241 ))
3
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242
6
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diff changeset
243 print(''' </conditional>
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diff changeset
244 </xml>''')
3
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245
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246 CHANGE_FORMAT_TPL = '''
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247 <xml name="efetch_formats">
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248 <change_format>
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249 {formats}
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iuc
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diff changeset
250 </change_format>
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iuc
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diff changeset
251 </xml>
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252 '''
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253
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iuc
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254 CHANGE_FORMAT_WHEN_TPL = '''<when input="output_format" value="{key}" format="{value}"/>'''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
255 # Format options
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256
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257
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iuc
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diff changeset
258 whens = []
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iuc
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diff changeset
259 for (k, v) in format_names.items():
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iuc
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diff changeset
260 if v is None:
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iuc
parents:
diff changeset
261 v = 'text'
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iuc
parents:
diff changeset
262 elif v == 'asn.1':
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iuc
parents:
diff changeset
263 v = 'asn1'
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iuc
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diff changeset
264
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iuc
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diff changeset
265 whens.append(CHANGE_FORMAT_WHEN_TPL.format(
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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diff changeset
266 key=k, value=v
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iuc
parents:
diff changeset
267 ))
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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268
6
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iuc
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diff changeset
269 print(CHANGE_FORMAT_TPL.format(formats='\n '.join(whens)))