Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

annotate data_manager/ncbi_taxonomy_fetcher.xml @ 0:078e803565cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
author devteam
date Fri, 06 Nov 2015 14:16:28 -0500
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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
devteam
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1 <?xml version="1.0"?>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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2 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.0">
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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3 <description>taxonomy downloader</description>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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4 <stdio>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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5 <exit_code description="Error" level="fatal" range="1:" />
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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6 </stdio>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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7 <command interpreter="python">
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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8 <![CDATA[
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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9 data_manager.py --out "${out_file}"
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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10 #if $taxonomy_url:
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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11 --url "${taxonomy_url}"
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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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
devteam
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13 #if $database_name:
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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14 --name "${database_name}"
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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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
devteam
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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
devteam
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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
devteam
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18 <inputs>
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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19 <param help="Enter a unique identifier, or leave blank for today's date" label="Name for this database" name="database_name" type="text" optional="True" />
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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20 <param label="Enter URL for taxonomy files" name="taxonomy_url" type="text" />
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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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>
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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23 <data format="data_manager_json" name="out_file" />
078e803565cf planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
devteam
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24 </outputs>
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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25 </tool>