Mercurial > repos > iuc > snpeff

annotate snpEff_download.xml @ 15:479c4f2f4826 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173
author iuc
date Mon, 09 Jul 2018 13:22:58 -0400
parents 5a29ab10dba6
children 65ae79bddc69
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1 <tool id="snpEff_download" name="SnpEff download:" version="@wrapper_version@.galaxy1">
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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 '$snpeff_db.files_path' -v '$genome_version'
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13 ]]></command>
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14 <inputs>
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15 <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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16 <help>@snpeff_database_url@</help>
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17 <validator type="regex" message="A genome version name is required">\S+</validator>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @snpeff_version@ ${genome_version}"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="genome_version" value="ebola_zaire"/>
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26 <output name="snpeff_db">
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27 <assert_contents>
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28 <has_text text="ebola_zaire" />
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29 </assert_contents>
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30 </output>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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35 **What it does**
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37 This tool downloads a specified database from @snpeff_database_url@. It deposits it into the history.
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39 -------
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41 .. class:: infomark
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43 **The usage scenario**
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45 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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47 #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box.
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48 #. 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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49
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50 @snpeff_in_galaxy_info@
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51 @external_documentation@
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52 ]]></help>
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53 <expand macro="citations" />
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54 </tool>