Mercurial > repos > iuc > ncbi_eutils_esummary
annotate __efetch_build_options.py @ 8:7fe990069458 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
author | iuc |
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date | Mon, 23 Jan 2023 10:37:10 +0000 |
parents | 254f40d3ae2b |
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92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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1 #!/usr/bin/env python |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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2 # Daniel Blankenberg |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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3 # Creates the options for tool interface |
1
c8d4ea6376a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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4 from __future__ import print_function |
c8d4ea6376a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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5 |
0
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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6 import re |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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7 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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8 # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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9 db_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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10 <DbName>annotinfo</DbName> |
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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11 <DbName>assembly</DbName> |
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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12 <DbName>bioproject</DbName> |
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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13 <DbName>biosample</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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14 <DbName>biosystems</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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15 <DbName>blastdbinfo</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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16 <DbName>books</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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17 <DbName>cdd</DbName> |
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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18 <DbName>clinvar</DbName> |
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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19 <DbName>clone</DbName> |
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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20 <DbName>dbvar</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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21 <DbName>gap</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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22 <DbName>gapplus</DbName> |
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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23 <DbName>gds</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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24 <DbName>gencoll</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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25 <DbName>gene</DbName> |
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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26 <DbName>genome</DbName> |
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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27 <DbName>geoprofiles</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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28 <DbName>grasp</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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29 <DbName>gtr</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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30 <DbName>homologene</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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31 <DbName>medgen</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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32 <DbName>mesh</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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33 <DbName>ncbisearch</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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34 <DbName>nlmcatalog</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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35 <DbName>nuccore</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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36 <DbName>nucest</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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37 <DbName>nucgss</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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38 <DbName>nucleotide</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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39 <DbName>omim</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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40 <DbName>orgtrack</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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41 <DbName>pcassay</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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42 <DbName>pccompound</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
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43 <DbName>pcsubstance</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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44 <DbName>pmc</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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45 <DbName>popset</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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46 <DbName>probe</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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47 <DbName>protein</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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48 <DbName>proteinclusters</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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49 <DbName>pubmed</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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50 <DbName>pubmedhealth</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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51 <DbName>seqannot</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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52 <DbName>snp</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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53 <DbName>sra</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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54 <DbName>structure</DbName> |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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55 <DbName>taxonomy</DbName> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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56 <DbName>unigene</DbName>'''.replace("<DbName>", "").replace("</DbName>", "").split("\n") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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57 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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58 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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59 help = ''' (all) |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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60 docsum xml Document Summary |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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61 docsum json Document Summary |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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62 full text Full Document |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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63 uilist xml Unique Identifier List |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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64 uilist text Unique Identifier List |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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65 full xml Full Document |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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66 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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67 bioproject |
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68 native BioProject Report |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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69 native xml RecordSet |
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70 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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71 biosample |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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72 native BioSample Report |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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73 native xml BioSampleSet |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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74 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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75 biosystems |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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76 native xml Sys-set |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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77 |
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78 gds |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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79 native xml RecordSet |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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|
80 summary 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
|
81 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
82 gene |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
83 gene_table xml Gene Table |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
84 native text Gene Report |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
85 native asn.1 Entrezgene |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
86 native xml Entrezgene-Set |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
87 tabular tabular Tabular Report |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
88 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
89 homologene |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
90 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
|
91 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
|
92 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
|
93 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
|
94 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
|
95 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
|
96 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
97 mesh |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
98 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
|
99 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
|
100 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
|
101 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
102 nlmcatalog |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
103 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
|
104 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
|
105 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
106 pmc |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
107 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
|
108 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
|
109 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
110 pubmed |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
111 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
|
112 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
|
113 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
|
114 native xml PubmedArticleSet |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
115 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
116 (sequences) |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
117 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:
diff
changeset
|
118 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:
diff
changeset
|
119 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
|
120 fasta xml TinySeq |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
121 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:
diff
changeset
|
122 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
|
123 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
|
124 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
|
125 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
|
126 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
|
127 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
|
128 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
|
129 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
|
130 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
|
131 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
|
132 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:
diff
changeset
|
133 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:
diff
changeset
|
134 ipg xml IPGReportSet |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
135 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:
diff
changeset
|
136 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
|
137 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
|
138 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
139 snp |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
140 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:
diff
changeset
|
141 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
|
142 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
|
143 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
|
144 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
|
145 native xml ExchangeSet |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
146 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:
diff
changeset
|
147 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:
diff
changeset
|
148 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
149 sra |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
150 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:
diff
changeset
|
151 runinfo xml SraRunInfo |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
152 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
153 structure |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
154 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:
diff
changeset
|
155 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:
diff
changeset
|
156 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
|
157 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
158 taxonomy |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
159 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:
diff
changeset
|
160 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:
diff
changeset
|
161 |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
162 |
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 = {} |
92bd8a680b9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
iuc
parents:
diff
changeset
|
164 for db_name in db_list: |
92bd8a680b9d
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165 db[db_name] = [] |
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166 |
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167 section = None |
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168 for line in help: |
1
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169 line = re.split(r'\s{2,}', line.strip()) |
0
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170 # Ignore empties |
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171 if len(line) == 0: |
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172 continue |
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173 # Section headers have one item |
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174 elif len(line) == 1: |
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175 section = line[0] |
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176 db[section] = [] |
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177 # Format lines have 2+ |
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178 elif len(line) == 2: |
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179 parent_format = line[0] |
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180 description = line[1] |
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181 |
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182 if parent_format not in db[section]: |
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183 db[section].append((parent_format, None, description)) |
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184 elif len(line) == 3: |
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185 parent_format = line[0] |
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186 format_modifier = line[1] |
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187 description = line[2] |
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188 |
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189 if parent_format not in db[section]: |
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190 db[section].append((parent_format, format_modifier, description)) |
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191 |
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192 |
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193 all_formats = db['(all)'] |
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194 del db['(all)'] |
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195 sequences_formats = db['(sequences)'] |
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196 del db['(sequences)'] |
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197 del db[''] |
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198 |
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199 for key in db: |
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200 db[key] += all_formats |
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201 |
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iuc
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202 for key in ('nuccore', 'nucest', 'nucgss', 'nucleotide'): |
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203 db[key] += sequences_formats |
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204 |
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205 MACRO_TPL = ''' |
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206 |
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207 ''' |
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208 |
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209 WHEN_TPL = ''' <when value="{format}"> |
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210 <param name="output_format" type="select" label="Output Format"> |
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211 {format_options} |
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212 </param> |
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213 </when>''' |
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214 |
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215 FORMAT_OPTION_TPL = '''<option value="{name_type}">{name_type_human}</option>''' |
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216 |
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217 format_names = {} |
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218 |
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219 print(''' <xml name="db"> |
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220 <conditional name="db"> |
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221 <expand macro="dbselect" />''') |
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222 for key in sorted(db): |
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223 format_options = [] |
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224 |
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225 for (parent_format, format_modifier, description) in sorted(db[key]): |
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226 name_human = description |
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227 if format_modifier: |
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228 name_human += ' (%s)' % format_modifier |
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229 format_string = '%s-%s' % (parent_format, format_modifier) |
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230 |
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231 format_options.append(FORMAT_OPTION_TPL.format( |
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232 name_type=format_string, |
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233 name_type_human=name_human, |
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234 )) |
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235 |
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236 format_names[format_string] = format_modifier |
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237 |
1
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238 print(WHEN_TPL.format( |
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239 format=key, |
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240 format_options='\n '.join(format_options) |
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241 )) |
0
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242 |
1
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243 print(''' </conditional> |
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244 </xml>''') |
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245 |
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246 CHANGE_FORMAT_TPL = ''' |
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247 <xml name="efetch_formats"> |
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248 <change_format> |
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249 {formats} |
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250 </change_format> |
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251 </xml> |
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252 ''' |
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253 |
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254 CHANGE_FORMAT_WHEN_TPL = '''<when input="output_format" value="{key}" format="{value}"/>''' |
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255 # Format options |
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256 |
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257 |
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258 whens = [] |
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259 for (k, v) in format_names.items(): |
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260 if v is None: |
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261 v = 'text' |
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262 elif v == 'asn.1': |
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263 v = 'asn1' |
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264 |
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265 whens.append(CHANGE_FORMAT_WHEN_TPL.format( |
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266 key=k, value=v |
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267 )) |
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268 |
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269 print(CHANGE_FORMAT_TPL.format(formats='\n '.join(whens))) |