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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 71b9c1035f713be174bfcf5ecb20804495f39258
author earlhaminst
date Thu, 07 Mar 2024 19:39:30 +0000
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03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
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1 <tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@VERSION@">
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2 <description>generates the ETE sqlite DB from the NCBI taxdump.tar.gz</description>
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3 <macros>
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4 <import>ete_macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 python '$__tool_directory__/ete_init_taxdb.py'
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10 #if $latestcond.latest == "local"
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11 -t '$latestcond.taxdump'
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12 #end if
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13 -d '$database'
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14 ]]></command>
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15 <inputs>
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16 <conditional name="latestcond">
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17 <param name="latest" type="select" label="Get latest version" help="Get the latest version of the taxdump from the NCBI website">
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18 <option value="local" selected="true">Use a local taxdump</option>
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19 <option value="latest">Get latest taxdump online</option>
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20 </param>
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21 <when value="local">
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22 <param name="taxdump" type="data" format="tar" label="NCBI taxdump" help="NCBI taxonomy database dump in tar.gz format" />
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23 </when>
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24 <when value="latest" />
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25 </conditional>
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26 </inputs>
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27 <outputs>
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28 <data name="database" format="sqlite" label="${tool.name} on ${on_string}" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="latest" value="local" />
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33 <param name="taxdump" ftype="tar" value="taxdump.tar.gz" />
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34 <output name="database" file="taxdump.sqlite" compare="sim_size" />
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 Generates the ETE sqlite data base from the NCBI taxdump.tar.gz using the `ETE Toolkit`_.
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40 .. _ETE Toolkit: http://etetoolkit.org/
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42 **Input**
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44 - NCBI taxdump: NCBI taxdump in tar.gz format. If not given the latest is downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
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46 **Output**
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47
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48 - *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>