Mercurial > repos > iuc > ncbi_entrez_direct_esearch

annotate __efetch_build_options.py @ 4:95b5c34650b6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1f7b04db717bd82f93519fdc3f34f589bb671e48
author iuc
date Mon, 29 Jul 2024 07:07:19 +0000
parents b6ffd64c448e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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1 #!/usr/bin/env python
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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2
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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3 # Daniel Blankenberg
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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4 # Creates the options for tool interface
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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5
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6 # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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7 db_list = '''<DbName>pubmed</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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8 <DbName>protein</DbName>
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9 <DbName>nuccore</DbName>
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10 <DbName>nucleotide</DbName>
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11 <DbName>nucgss</DbName>
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12 <DbName>nucest</DbName>
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13 <DbName>structure</DbName>
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14 <DbName>genome</DbName>
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15 <DbName>annotinfo</DbName>
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16 <DbName>assembly</DbName>
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17 <DbName>bioproject</DbName>
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18 <DbName>biosample</DbName>
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19 <DbName>blastdbinfo</DbName>
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20 <DbName>books</DbName>
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21 <DbName>cdd</DbName>
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22 <DbName>clinvar</DbName>
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23 <DbName>clone</DbName>
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24 <DbName>gap</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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25 <DbName>gapplus</DbName>
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26 <DbName>grasp</DbName>
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27 <DbName>dbvar</DbName>
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28 <DbName>gene</DbName>
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29 <DbName>gds</DbName>
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30 <DbName>geoprofiles</DbName>
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31 <DbName>homologene</DbName>
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32 <DbName>medgen</DbName>
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33 <DbName>mesh</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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34 <DbName>ncbisearch</DbName>
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35 <DbName>nlmcatalog</DbName>
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36 <DbName>omim</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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37 <DbName>orgtrack</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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38 <DbName>pmc</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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39 <DbName>popset</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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40 <DbName>probe</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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41 <DbName>proteinclusters</DbName>
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42 <DbName>pcassay</DbName>
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43 <DbName>biosystems</DbName>
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44 <DbName>pccompound</DbName>
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45 <DbName>pcsubstance</DbName>
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46 <DbName>pubmedhealth</DbName>
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47 <DbName>seqannot</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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48 <DbName>snp</DbName>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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49 <DbName>sra</DbName>
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50 <DbName>taxonomy</DbName>
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51 <DbName>unigene</DbName>
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52 <DbName>gencoll</DbName>
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53 <DbName>gtr</DbName>'''.replace("<DbName>", "").replace("</DbName>", "").split("\n")
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54
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55
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56 help = ''' (all)
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57 docsum DocumentSummarySet XML
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58 docsum json DocumentSummarySet JSON
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59 full Same as native except for mesh
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60 uid Unique Identifier List
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61 url Entrez URL
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62 xml Same as -format full -mode xml
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63
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64 bioproject
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65 native BioProject Report
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66 native xml RecordSet XML
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67
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68 biosample
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69 native BioSample Report
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70 native xml BioSampleSet XML
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71
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72 biosystems
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73 native xml Sys-set XML
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74
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75 gds
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76 native xml RecordSet XML
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77 summary Summary
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78
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79 gene
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80 gene_table Gene Table
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81 native Gene Report
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82 native asn.1 Entrezgene ASN.1
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83 native xml Entrezgene-Set XML
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84 tabular Tabular Report
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85
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86 homologene
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87 alignmentscores Alignment Scores
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diff changeset
88 fasta FASTA
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
89 homologene Homologene Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
90 native Homologene List
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
91 native asn.1 HG-Entry ASN.1
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
92 native xml Entrez-Homologene-Set XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
93
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
94 mesh
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
95 full Full Record
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
96 native MeSH Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
97 native xml RecordSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
98
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
99 nlmcatalog
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
100 native Full Record
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
101 native xml NLMCatalogRecordSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
102
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
103 pmc
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
104 medline MEDLINE
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
105 native xml pmc-articleset XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
106
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
107 pubmed
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
108 abstract Abstract
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
109 medline MEDLINE
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
110 native asn.1 Pubmed-entry ASN.1
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
111 native xml PubmedArticleSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
112
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
113 (sequences)
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
114 acc Accession Number
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
115 est EST Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
116 fasta FASTA
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
117 fasta xml TinySeq XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
118 fasta_cds_aa FASTA of CDS Products
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
119 fasta_cds_na FASTA of Coding Regions
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
120 ft Feature Table
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
121 gb GenBank Flatfile
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
122 gb xml GBSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
123 gbc xml INSDSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
124 gbwithparts GenBank with Contig Sequences
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
125 gene_fasta FASTA of Gene
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
126 gp GenPept Flatfile
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
127 gp xml GBSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
128 gpc xml INSDSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
129 gss GSS Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
130 ipg Identical Protein Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
131 ipg xml IPGReportSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
132 native text Seq-entry ASN.1
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
133 native xml Bioseq-set XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
134 seqid Seq-id ASN.1
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
135
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
136 snp
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
137 chr Chromosome Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
138 docset Summary
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
139 fasta FASTA
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
140 flt Flat File
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
141 native asn.1 Rs ASN.1
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
142 native xml ExchangeSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
143 rsr RS Cluster Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
144 ssexemplar SS Exemplar List
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
145
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
146 sra
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
147 native xml EXPERIMENT_PACKAGE_SET XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
148 runinfo xml SraRunInfo XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
149
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
150 structure
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
151 mmdb Ncbi-mime-asn1 strucseq ASN.1
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
152 native MMDB Report
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
153 native xml RecordSet XML
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
154
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
155 taxonomy
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
156 native Taxonomy List
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
157 native xml TaxaSet XML'''.split("\n")
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
158
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
159 db = {}
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
160 name = None
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
161 all = "(all)"
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
162 for line in help:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
163 if line.strip() and line[2] != ' ':
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
164 name = line.strip()
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
165 db[name] = {}
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
166 elif line.strip():
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
167 format = line[0:len(" docsum ")].strip()
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
168 mode = line[len(" docsum "):len(" docsum json ")].strip()
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
169 if format not in db[name]:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
170 db[name][format] = []
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
171 db[name][format].append(mode)
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
172
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
173 for name in db_list:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
174 if name not in db:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
175 db[name] = {}
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
176
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
177 db["sequences"] = db["(sequences)"]
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
178 del db["(sequences)"]
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
179
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
180 print('<conditional name="db">')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
181 print(' <param name="db" type="select" label="Database" argument="-db">')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
182 for name in sorted(db.keys()):
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
183 if name == all:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
184 continue
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
185 print(' <option value="%s">%s</option>' % (name, name))
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
186 print(' <option value="">Manual Entry</option>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
187 print(' </param>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
188
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
189 for name in sorted(db.keys()):
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
190 if name == all:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
191 continue
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
192 my_dict = db[all].copy()
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
193
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
194 for format, modes in db[name].items():
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
195 if format in my_dict:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
196 for mode in modes:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
197 if mode not in my_dict[format]:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
198 my_dict[format].append(mode)
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
199 else:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
200 my_dict[format] = modes
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
201 if "" not in my_dict:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
202 my_dict[""] = [""]
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
203 print(' <when value="%s">' % name)
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
204 print(' <conditional name="format">')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
205 print(' <param name="format" type="select" label="Format" argument="-format">')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
206 for format in sorted(my_dict.keys()):
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
207 print(' <option value="%s">%s</option>' % (format, format or "None"))
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
208 print(' </param>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
209 for format in sorted(my_dict.keys()):
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
210 print(' <when value="%s">' % format)
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
211 print(' <param name="mode" type="select" label="Mode" argument="-mode">')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
212 if "" not in my_dict[format]:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
213 my_dict[format].append("")
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
214 for mode in sorted(my_dict[format]):
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
215 print(' <option value="%s">%s</option>' % (mode, mode or "None"))
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
216 print(' </param>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
217 print(' </when>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
218 print(' </conditional>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
219 print(' </when>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
220 print(' <when value="">')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
221 print(' <param name="db_manual" type="text" label="Database" argument="-db"/>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
222 print(' <param name="format" type="text" label="Format" argument="-format"/>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
223 print(' <param name="mode" type="text" label="Mode" argument="-mode"/>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
224 print(' </when>')
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
iuc
parents:
diff changeset
225 print('</conditional>')