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annotate ete_init_taxdb.xml @ 13:ed74587a13c8 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 23b3c7c09a7d391b576e3b19f8b34dd63d636bdc
author earlhaminst
date Thu, 01 Sep 2022 16:11:32 +0000
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children d40b9a7debe5
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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="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/ete_init_taxdb.py'
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9 #if $latestcond.latest == "local"
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10 -t '$latestcond.taxdump'
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11 #end if
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12 -d '$database'
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13 ]]></command>
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14 <inputs>
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15 <conditional name="latestcond">
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16 <param name="latest" type="select" label="Get latest version" help="Get the latest version of the taxdump from the NCBI website">
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17 <option value="local" selected="true">Use a local taxdump</option>
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18 <option value="latest">Get latest taxdump online</option>
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19 </param>
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20 <when value="local">
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21 <param name="taxdump" type="data" format="tar" label="NCBI taxdump" help="NCBI taxonomy database dump in tar.gz format" />
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22 </when>
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23 <when value="latest" />
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24 </conditional>
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25 </inputs>
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26 <outputs>
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27 <data name="database" format="sqlite" label="${tool.name} on ${on_string}" />
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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="latest" value="local" />
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32 <param name="taxdump" ftype="tar" value="taxdump.tar.gz" />
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33 <output name="database" file="taxdump.sqlite" compare="sim_size" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 Generates the ETE sqlite data base from the NCBI taxdump.tar.gz using the `ETE Toolkit`_.
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39 .. _ETE Toolkit: http://etetoolkit.org/
2
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41 **Input**
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43 - 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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45 **Output**
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46
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47 - *(ETE3) Taxonomy Database* a sqlite database that has been created by ETE from the NCBI taxonomy dump
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>