Mercurial > repos > devteam > data_manager_fetch_ncbi_taxonomy

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit a54e50916ebdb0858b049cdc549a43df801e1a71
author iuc
date Tue, 21 May 2024 07:36:09 +0000
parents 6dd9e00dea95
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fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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1 <?xml version="1.0"?>
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2 <tool id="ncbi_taxonomy_fetcher" name="NCBI" tool_type="manage_data" version="1.0.4" profile="23.0">
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3 <description>taxonomy downloader</description>
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4 <requirements>
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5 <requirement type="package" version="3.7">python</requirement>
9de2fb1ce1fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/data_manager.py' --out '${out_file}'
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10 #if $taxonomy_url:
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11 --url '${taxonomy_url}'
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12 #end if
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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13 #if $database_name:
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14 --name '${database_name}'
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15 #end if
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16 $name_maps
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17 $partial_data
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18 ]]>
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19 </command>
fafcd2f5db36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
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20 <inputs>
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21 <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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22 <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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23 <param name="name_maps" type="boolean" truevalue="--name-maps" falsevalue="" label="Also download accession2taxid data" checked="false" />
6dd9e00dea95 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_ncbi_taxonomy/ commit 3d78021971b83d585c432830cee0488ada7bd257"
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24 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
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25 </inputs>
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26 <outputs>
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27 <data name="out_file" format="data_manager_json" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="database_name" value="tax_name"/>
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32 <output name="out_file" value="taxonomy.json"/>
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33 </test>
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34 <test>
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35 <param name="database_name" value="tax_name"/>
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36 <param name="name_maps" value="true"/>
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37 <param name="partial_data" value="--partial"/>
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38 <output name="out_file" value="taxonomy_with_accession2taxid.json"/>
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39 </test>
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40 </tests>
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41 <help>
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42 Download a taxonomy dump from a provided URL.
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43 The default URL is the latest dump from NCBI taxonomy.
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44 The accession2taxid data comes from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ and can be used by the Diamond data_manager (uses ~20Gb as of 2021).
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45 </help>
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46 </tool>