Mercurial > repos > iuc > snpeff

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5
author iuc
date Sat, 04 Oct 2025 17:00:46 +0000
parents ebe9fd7e5bd1
children
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1 <tool id="snpEff_download" name="SnpEff download:" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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2 <description> download a pre-built database</description>
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3 <macros>
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4 <import>snpEff_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="requirement" />
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8 </requirements>
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command><![CDATA[
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12 snpEff download -dataDir "\$PWD/temp" -v '$genome_version' &&
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13 mkdir -p '$snpeff_db.files_path' &&
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14 mv temp/'$genome_version' '$snpeff_db.files_path'
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15 ]]></command>
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16 <inputs>
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17 <param name="genome_version" type="text" value="" label="Select the annotation database you want to download (e.g. GRCh38.86, mm10 etc.)" help="The list of available databases can be obtained with 'SnpEff databases' tool">
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18 <validator type="empty_field" message="A genome version name is required" />
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data name="snpeff_db" format="snpeffdb" label="@SNPEFF_VERSION@ ${genome_version} database"/>
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23 </outputs>
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24 <tests>
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25 <test expect_failure="true">
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26 <!-- The only meaningful test for this tool currently often, but not always, fails
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27 when run from github because the download attempt from github gets blocked
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28 by the data provider.
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29 As a workaround we make the test fail consistently.
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30 Put the "e" back on "zair" for an actual download attempt. -->
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31 <param name="genome_version" value="ebola_zair"/>
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32 <!-- then also uncomment the ouput assertion
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33 <output name="snpeff_db">
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34 <assert_contents>
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35 <has_text text="ebola_zaire" />
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36 </assert_contents>
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37 </output>
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38 -->
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 **What it does**
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43
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44 This tool downloads a specified database from a remote SnpEff repository. It deposits it into the history.
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46 -------
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48 .. class:: infomark
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50 **The usage scenario**
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52 Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can:
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54 #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box.
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55 #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter.
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57 @SNPEFF_IN_GALAXY_INFO@
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58 @EXTERNAL_DOCUMENTATION@
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59 ]]></help>
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60 <expand macro="citations" />
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61 </tool>