Mercurial > repos > iuc > ncbi_eutils_esummary

annotate __efetch_build_options.py @ 0:92bd8a680b9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:41:02 -0400
parents
children c8d4ea6376a7
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92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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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
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4 import re
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5
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6 # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
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7 db_list = '''
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8 <DbName>annotinfo</DbName>
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9 <DbName>assembly</DbName>
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10 <DbName>bioproject</DbName>
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11 <DbName>biosample</DbName>
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12 <DbName>biosystems</DbName>
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13 <DbName>blastdbinfo</DbName>
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14 <DbName>books</DbName>
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15 <DbName>cdd</DbName>
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16 <DbName>clinvar</DbName>
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17 <DbName>clone</DbName>
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18 <DbName>dbvar</DbName>
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19 <DbName>gap</DbName>
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20 <DbName>gapplus</DbName>
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21 <DbName>gds</DbName>
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22 <DbName>gencoll</DbName>
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23 <DbName>gene</DbName>
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24 <DbName>genome</DbName>
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25 <DbName>geoprofiles</DbName>
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26 <DbName>grasp</DbName>
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27 <DbName>gtr</DbName>
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28 <DbName>homologene</DbName>
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29 <DbName>medgen</DbName>
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30 <DbName>mesh</DbName>
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31 <DbName>ncbisearch</DbName>
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32 <DbName>nlmcatalog</DbName>
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33 <DbName>nuccore</DbName>
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34 <DbName>nucest</DbName>
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35 <DbName>nucgss</DbName>
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36 <DbName>nucleotide</DbName>
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37 <DbName>omim</DbName>
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38 <DbName>orgtrack</DbName>
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39 <DbName>pcassay</DbName>
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40 <DbName>pccompound</DbName>
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41 <DbName>pcsubstance</DbName>
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42 <DbName>pmc</DbName>
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43 <DbName>popset</DbName>
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44 <DbName>probe</DbName>
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45 <DbName>protein</DbName>
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46 <DbName>proteinclusters</DbName>
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47 <DbName>pubmed</DbName>
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48 <DbName>pubmedhealth</DbName>
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49 <DbName>seqannot</DbName>
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50 <DbName>snp</DbName>
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51 <DbName>sra</DbName>
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52 <DbName>structure</DbName>
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53 <DbName>taxonomy</DbName>
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54 <DbName>unigene</DbName>'''.replace( "<DbName>", "").replace( "</DbName>", "").split("\n")
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57 help = ''' (all)
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58 docsum xml Document Summary
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59 docsum json Document Summary
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60 full text Full Document
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61 uilist xml Unique Identifier List
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62 uilist text Unique Identifier List
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63 full xml Full Document
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65 bioproject
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66 native BioProject Report
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67 native xml RecordSet
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69 biosample
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70 native BioSample Report
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71 native xml BioSampleSet
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73 biosystems
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74 native xml Sys-set
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76 gds
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77 native xml RecordSet
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78 summary text Summary
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80 gene
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81 gene_table xml Gene Table
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82 native text Gene Report
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83 native asn.1 Entrezgene
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84 native xml Entrezgene-Set
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85 tabular tabular Tabular Report
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87 homologene
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
88 alignmentscores text Alignment Scores
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
89 fasta fasta FASTA
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
90 homologene text Homologene Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
91 native text Homologene List
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
92 native asn.1 HG-Entry
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
93 native xml Entrez-Homologene-Set
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
94
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
95 mesh
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
96 full text Full Record
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
97 native text MeSH Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
98 native xml RecordSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
99
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
100 nlmcatalog
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
101 native text Full Record
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
102 native xml NLMCatalogRecordSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
103
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
104 pmc
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
105 medline text MEDLINE
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
106 native xml pmc-articleset
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
107
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
108 pubmed
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
109 abstract xml Abstract
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
110 medline text MEDLINE
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
111 native asn.1 Pubmed-entry
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
112 native xml PubmedArticleSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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113
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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114 (sequences)
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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115 acc text Accession Number
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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116 est xml EST Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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117 fasta fasta FASTA
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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118 fasta xml TinySeq
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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119 fasta_cds_aa fasta CDS Products
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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120 fasta_cds_na fasta Coding Regions
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
121 ft text Feature Table
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
122 gb text GenBank Flatfile
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
123 gb xml GBSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
124 gbc xml INSDSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
125 gbwithparts text GenBank with Contig Sequences
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
126 gene_fasta fasta FASTA of Gene
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
127 gp text GenPept Flatfile
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
128 gp xml GBSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
129 gpc xml INSDSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
130 gss text GSS Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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131 ipg text Identical Protein Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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132 ipg xml IPGReportSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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133 native text Seq-entry
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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134 native xml Bioseq-set
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
135 seqid asn.1 Seq-id
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
136
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
137 snp
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
138 chr text Chromosome Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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139 docset text Summary
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
140 fasta fasta FASTA
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
141 flt text Flat File
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
142 native asn.1 Rs
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
143 native xml ExchangeSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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144 rsr tabular RS Cluster Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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145 ssexemplar text SS Exemplar List
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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146
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
147 sra
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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148 native xml EXPERIMENT_PACKAGE_SET
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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149 runinfo xml SraRunInfo
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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150
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
151 structure
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
152 mmdb asn.1 Ncbi-mime-asn1 strucseq
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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153 native text MMDB Report
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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154 native xml RecordSet
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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155
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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156 taxonomy
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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157 native text Taxonomy List
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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158 native xml TaxaSet'''.split("\n")
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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159
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
160
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
161 db = {}
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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162 for db_name in db_list:
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
163 db[db_name] = []
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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164
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
165 section = None
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
166 for line in help:
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
167 line = re.split('\s{2,}', line.strip())
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
168 # Ignore empties
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
169 if len(line) == 0:
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
170 continue
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
171 # Section headers have one item
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
172 elif len(line) == 1:
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
173 section = line[0]
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
174 db[section] = []
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
175 # Format lines have 2+
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
176 elif len(line) == 2:
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
177 parent_format = line[0]
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
178 description = line[1]
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179
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iuc
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180 if parent_format not in db[section]:
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iuc
parents:
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181 db[section].append((parent_format, None, description))
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iuc
parents:
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182 elif len(line) == 3:
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iuc
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183 parent_format = line[0]
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iuc
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184 format_modifier = line[1]
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iuc
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185 description = line[2]
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186
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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187 if parent_format not in db[section]:
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iuc
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188 db[section].append((parent_format, format_modifier, description))
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189
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190
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iuc
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191 all_formats = db['(all)']
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iuc
parents:
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192 del db['(all)']
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iuc
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193 sequences_formats = db['(sequences)']
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194 del db['(sequences)']
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195 del db['']
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196
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iuc
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197 for key in db:
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198 db[key] += all_formats
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199
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iuc
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200 for key in ('nuccore', 'nucest', 'nucgss', 'nucleotide'):
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iuc
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201 db[key] += sequences_formats
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iuc
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202
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iuc
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203 MACRO_TPL = '''
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iuc
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204
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iuc
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205 '''
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iuc
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206
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iuc
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207 WHEN_TPL = ''' <when value="{format}">
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iuc
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208 <param name="output_format" type="select" label="Output Format">
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iuc
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209 {format_options}
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iuc
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210 </param>
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iuc
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211 </when>'''
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212
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iuc
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213 FORMAT_OPTION_TPL = '''<option value="{name_type}">{name_type_human}</option>'''
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214
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iuc
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215 format_names = {}
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iuc
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216
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217 print ''' <xml name="db">
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218 <conditional name="db">
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iuc
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219 <expand macro="dbselect" />'''
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iuc
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220 for key in sorted(db):
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iuc
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221 format_options = []
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iuc
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222
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iuc
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223 for (parent_format, format_modifier, description) in sorted(db[key]):
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iuc
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224 name_human = description
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iuc
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225 if format_modifier:
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iuc
parents:
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226 name_human += ' (%s)' % format_modifier
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iuc
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227 format_string = '%s-%s' % (parent_format, format_modifier)
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228
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iuc
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229 format_options.append(FORMAT_OPTION_TPL.format(
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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230 name_type=format_string,
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iuc
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231 name_type_human=name_human,
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iuc
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232 ))
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233
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234 format_names[format_string] = format_modifier
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235
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
236 print WHEN_TPL.format(
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
237 format=key,
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iuc
parents:
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238 format_options='\n '.join(format_options)
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iuc
parents:
diff changeset
239 )
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iuc
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240
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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241 print ''' </conditional>
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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242 </xml>'''
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iuc
parents:
diff changeset
243
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
244 CHANGE_FORMAT_TPL = '''
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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245 <xml name="efetch_formats">
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iuc
parents:
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246 <change_format>
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iuc
parents:
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247 {formats}
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iuc
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248 </change_format>
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iuc
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diff changeset
249 </xml>
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iuc
parents:
diff changeset
250 '''
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
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251
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
252 CHANGE_FORMAT_WHEN_TPL = '''<when input="output_format" value="{key}" format="{value}"/>'''
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
253 # Format options
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iuc
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254
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iuc
parents:
diff changeset
255
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
256 whens = []
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
257 for (k, v) in format_names.items():
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iuc
parents:
diff changeset
258 if v is None:
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iuc
parents:
diff changeset
259 v = 'text'
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iuc
parents:
diff changeset
260 elif v == 'asn.1':
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iuc
parents:
diff changeset
261 v = 'asn1'
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iuc
parents:
diff changeset
262
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
263 whens.append(CHANGE_FORMAT_WHEN_TPL.format(
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
264 key=k, value=v
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iuc
parents:
diff changeset
265 ))
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
266
92bd8a680b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff changeset
267 print CHANGE_FORMAT_TPL.format(formats='\n '.join(whens))