Mercurial > repos > iuc > snpeff

annotate snpEff_download.xml @ 32:ebe9fd7e5bd1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 280d5247becaa9a70db9c5c4a2f1fc50d302838a
author iuc
date Mon, 18 Nov 2024 22:15:18 +0000
parents b7029a54f73e
children 94653948fdb9
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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>
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26 <param name="genome_version" value="ebola_zaire"/>
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27 <output name="snpeff_db">
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28 <assert_contents>
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29 <has_text text="ebola_zaire" />
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30 </assert_contents>
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31 </output>
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32 </test>
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33 <test>
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34 <param name="genome_version" value="Bdellovibrio_bacteriovorus_hd100"/>
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35 <output name="snpeff_db">
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36 <assert_contents>
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37 <has_text text="Bdellovibrio_bacteriovorus_hd100" />
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38 </assert_contents>
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39 </output>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 **What it does**
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44
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45 This tool downloads a specified database from a remote SnpEff repository. It deposits it into the history.
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47 -------
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49 .. class:: infomark
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51 **The usage scenario**
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53 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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55 #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box.
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56 #. 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
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58 @SNPEFF_IN_GALAXY_INFO@
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59 @EXTERNAL_DOCUMENTATION@
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60 ]]></help>
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61 <expand macro="citations" />
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62 </tool>