Mercurial > repos > iuc > snpeff

annotate snpEff_macros.xml @ 12:5a29ab10dba6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
author iuc
date Thu, 29 Mar 2018 20:39:49 -0400
parents 5b4ac70948d2
children 479c4f2f4826
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1 <macros>
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2 <xml name="requirement">
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3 <requirement type="package" version="4.3.1t">snpeff</requirement>
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4 </xml>
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5 <xml name="stdio">
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6 <stdio>
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7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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8 <exit_code range="1:" level="fatal" description="Error" />
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9 </stdio>
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10 </xml>
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11 <xml name="version_command">
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12 <version_command><![CDATA[
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13 snpEff -version
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14 ]]></version_command>
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15 </xml>
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16 <token name="@wrapper_version@">4.3+T</token>
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17 <token name="@snpeff_version@">SnpEff4.3</token>
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18 <token name="@snpeff_database_url@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
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19 <token name="@java_options@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
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20 <token name="@external_documentation@">
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23 -------
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25 To learn more about snpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
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26 </token>
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27 <token name="@snpeff_in_galaxy_info@">
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31 .. class:: warningmark
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33 **Using SnpEff in Galaxy: A few points to remember**
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35 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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37 **Pre-cached databases**
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39 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 **SbpEff eff** tool.
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41 In you *do not see them* keep reading...
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43 **Download pre-built databases**
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45 SnpEff project generates large numbers of pre-build databases. These are available at @SNPEFF_DATABASE_URL@ and can downloaded. Follow these steps:
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47 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
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48 #. Use **SnpEff download** tool to download the database.
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49 #. 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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51 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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53 **Create your own database**
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55 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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57 #. Download Genbank record corresponding to your genome of interest from NCBI.
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58 #. Use **SnpEff build** to create the database.
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59 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
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61 Creating custom database has one benefit. The **SnpEff build** tool normally produces two outputs: (1) a SnpEff database and (2) FASTA file containing sequences from the Genbank file. If you are performing your experiment from the beginning by mapping reads against a genome and finding variants before annotating them with SnpEff you can use **this FASTA file** as a reference to map your reads against. This will guarantee that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.
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63 </token>
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67 <xml name="citations">
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68 <citations>
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69 <citation type="doi">10.4161/fly.19695</citation>
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70 <yield />
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71 </citations>
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72 </xml>
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73 </macros>