Mercurial > repos > iuc > ncbi_eutils_efetch

annotate __efetch_build_options.py @ 5:e269b3b5185b 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 02:37:49 -0400
parents aa88712a7536
children 2ff5369b4b51
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3
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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
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88 alignmentscores text Alignment Scores
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89 fasta fasta FASTA
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90 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
91 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
92 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
93 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
94
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
95 mesh
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
96 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
97 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
98 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
99
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
100 nlmcatalog
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
101 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
102 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
103
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
104 pmc
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
105 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
106 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
107
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iuc
parents:
diff changeset
108 pubmed
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
109 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
110 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
111 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
112 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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113
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iuc
parents:
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114 (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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115 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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116 est xml EST Report
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 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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118 fasta xml TinySeq
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iuc
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diff changeset
119 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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120 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
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121 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
122 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
123 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
124 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
125 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
126 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
127 gp text GenPept Flatfile
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
128 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
129 gpc 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
130 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
131 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
132 ipg xml IPGReportSet
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
133 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
134 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
135 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
136
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
137 snp
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
138 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
139 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
140 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
141 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
142 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
143 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
144 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
145 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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146
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
147 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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148 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
149 runinfo xml SraRunInfo
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iuc
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150
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iuc
parents:
diff changeset
151 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
152 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
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153 native text MMDB Report
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 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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155
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
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156 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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157 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:
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158 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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159
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iuc
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160
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iuc
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161 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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162 for db_name in db_list:
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iuc
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diff changeset
163 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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diff changeset
164
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iuc
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165 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
166 for line in help:
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iuc
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167 line = re.split('\s{2,}', line.strip())
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 # 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
169 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
170 continue
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
171 # 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
172 elif len(line) == 1:
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iuc
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diff changeset
173 section = 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
174 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
175 # 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
176 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
177 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
178 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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179
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iuc
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180 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
181 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
parents:
diff changeset
182 elif len(line) == 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
183 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
184 format_modifier = line[1]
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
185 description = line[2]
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
186
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
187 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
188 db[section].append((parent_format, format_modifier, description))
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
189
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
190
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
191 all_formats = db['(all)']
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
192 del db['(all)']
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
193 sequences_formats = db['(sequences)']
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
194 del db['(sequences)']
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
195 del db['']
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
196
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
197 for key in db:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
198 db[key] += all_formats
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
199
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
200 for key in ('nuccore', 'nucest', 'nucgss', 'nucleotide'):
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
201 db[key] += sequences_formats
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
202
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
203 MACRO_TPL = '''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
204
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
205 '''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
206
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
207 WHEN_TPL = ''' <when value="{format}">
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
208 <param name="output_format" type="select" label="Output Format">
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
209 {format_options}
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
210 </param>
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
211 </when>'''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
212
5
e269b3b5185b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents: 3
diff changeset
213 FORMAT_OPTION_TPL = '''<option value="{name_type}">{name_type_human}</option>'''
3
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
214
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
215 format_names = {}
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
216
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
217 print ''' <xml name="db">
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
218 <conditional name="db">
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
219 <expand macro="dbselect" />'''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
220 for key in sorted(db):
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
221 format_options = []
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
222
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
223 for (parent_format, format_modifier, description) in sorted(db[key]):
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
224 name_human = description
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
225 if format_modifier:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
226 name_human += ' (%s)' % format_modifier
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
227 format_string = '%s-%s' % (parent_format, format_modifier)
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
228
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
229 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
parents:
diff changeset
230 name_type=format_string,
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
231 name_type_human=name_human,
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
232 ))
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
233
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
234 format_names[format_string] = format_modifier
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
235
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
236 print WHEN_TPL.format(
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
237 format=key,
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
238 format_options='\n '.join(format_options)
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
239 )
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
240
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
241 print ''' </conditional>
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
242 </xml>'''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
243
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
244 CHANGE_FORMAT_TPL = '''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
245 <xml name="efetch_formats">
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
246 <change_format>
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
247 {formats}
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
248 </change_format>
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
249 </xml>
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
250 '''
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
251
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
252 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
parents:
diff changeset
253 # Format options
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
254
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
255
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
256 whens = []
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
257 for (k, v) in format_names.items():
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
258 if v is None:
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
259 v = 'text'
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
260 elif v == 'asn.1':
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
261 v = 'asn1'
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
262
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
263 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
parents:
diff changeset
264 key=k, value=v
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
265 ))
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
266
aa88712a7536 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
iuc
parents:
diff changeset
267 print CHANGE_FORMAT_TPL.format(formats='\n '.join(whens))