Mercurial > repos > iuc > snpeff

annotate snpEff_macros.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 <macros>
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2 <token name="@TOOL_VERSION@">5.2</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@SNPEFF_VERSION@">SnpEff5.2</token>
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5 <xml name="requirement">
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6 <requirement type="package" version="@TOOL_VERSION@">snpeff</requirement>
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7 <yield/>
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8 </xml>
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9 <xml name="stdio">
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10 <stdio>
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11 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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12 <exit_code range="1:" level="fatal" description="Error" />
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13 </stdio>
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14 </xml>
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15 <xml name="version_command">
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16 <version_command><![CDATA[
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17 snpEff -version
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18 ]]></version_command>
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19 </xml>
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20 <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
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21 <xml name="ref_select">
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22 <conditional name="reference_source">
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23 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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24 <option value="cached">Locally cached</option>
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25 <option value="history">History</option>
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26 </param>
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27 <when value="cached">
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28 <param name="ref_file" type="select" label="Select reference genome">
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29 <options from_data_table="fasta_indexes"/>
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30 </param>
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31 </when>
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32 <when value="history">
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33 <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/>
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34 </when>
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35 </conditional>
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36 </xml>
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37 <token name="@EXTERNAL_DOCUMENTATION@">
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40 -------
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42 To learn more about snpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
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43 </token>
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44 <token name="@SNPEFF_IN_GALAXY_INFO@">
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48 .. class:: warningmark
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50 **Using SnpEff in Galaxy: A few points to remember**
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52 SnpEff relies on specially formatted databases to generate annotations. It will not work without them. There are several ways in which these databases can be obtained.
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54 **Pre-cached databases**
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b1b327f475ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4366b6a23223f84039a0590cf0d7079b83d8f84"
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56 Many standard (e.g., human, mouse, *Drosophila*) databases are likely pre-cached within a given Galaxy instance. You should be able to see them listed in **Genome** drop-down of **SnpEff eff** tool.
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58 In you *do not see them* keep reading...
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60 **Download pre-built databases**
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62 SnpEff project generates large numbers of pre-build databases. To obtain and use them follow these steps:
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64 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
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65 #. Use **SnpEff download** tool to download the database.
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66 #. Finally, 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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68 Alternatively, you can specify the name of the database directly in **SnpEff eff** using the *Download on demand* option (again, **Genome source** parameter). In this case snpEff will download the database before performing annotation.
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70 **Create your own database**
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72 In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need:
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74 #. Download Genbank record corresponding to your genome of interest from NCBI or use annotations in GFF format accompanied by the corresponding genome in FASTA format.
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75 #. Use **SnpEff build** to create the database.
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76 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
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78 Creating custom database has one major advantage. It guaranteess that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.
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80 </token>
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83
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84 <xml name="citations">
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85 <citations>
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86 <citation type="doi">10.4161/fly.19695</citation>
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87 <yield />
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88 </citations>
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89 </xml>
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90 </macros>