Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

annotate data_manager/ncbi_taxonomy_fetcher.xml @ 3:f7b443a73374 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
author iuc
date Mon, 06 Jul 2020 23:29:44 +0000
parents 3d628f1e1bef
children cef5c909ccb8
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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1 <?xml version="1.0"?>
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f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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2 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.2">
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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3 <description>taxonomy downloader</description>
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f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
iuc
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4 <requirements>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
iuc
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5 <requirement type="package" version="3.7">python</requirement>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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6 </requirements>
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iuc
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7 <command detect_errors="exit_code">
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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8 <![CDATA[
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8dd4076813ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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9 python '$__tool_directory__/data_manager.py' --out '${out_file}'
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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10 #if $taxonomy_url:
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8dd4076813ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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11 --url '${taxonomy_url}'
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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12 #end if
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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13 #if $database_name:
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8dd4076813ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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14 --name '${database_name}'
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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15 #end if
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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16 ]]>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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17 </command>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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18 <inputs>
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19 <param name="database_name" type="text" optional="true" label="Name for this database" help="Enter a unique identifier, or leave blank for today's date" />
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3d628f1e1bef "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 04825a097d217d30deb5fcb6906fe718023e25b6"
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20 <param name="taxonomy_url" type="text" value='ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz' label="Enter URL for taxonomy files" />
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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21 </inputs>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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22 <outputs>
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8dd4076813ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 8652f36a3a3838dca989426961561e81432acf4f
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23 <data name="out_file" format="data_manager_json" />
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078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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24 </outputs>
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25 <tests>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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26 <test>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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27 <param name="database_name" value="tax_name"/>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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28 <param name="database_id" value="tax_id"/>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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29 <output name="out_file" value="taxonomy.json"/>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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30 </test>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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31 </tests>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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32 <help>
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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33 Download a taxonomy dump from a provided URL.
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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34 The default URL is the latest dump from NCBI taxonomy.
f7b443a73374 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 1bcd553f81064957d5786302361675c29ed58a8d"
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35 </help>
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36 </tool>