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comparison snpEff_macros.xml @ 16:7c4ede6d88a2 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 20:39:33 -0400
parents a7c106b938dd
children 718842784732
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15:ade43aeb0d40 16:7c4ede6d88a2
11 <xml name="version_command"> 11 <xml name="version_command">
12 <version_command><![CDATA[ 12 <version_command><![CDATA[
13 snpEff -version 13 snpEff -version
14 ]]></version_command> 14 ]]></version_command>
15 </xml> 15 </xml>
16 <token name="@wrapper_version@">4.3.1t</token> 16 <token name="@wrapper_version@">4.3+T</token>
17 <token name="@snpeff_version@">SnpEff4.3</token> 17 <token name="@snpeff_version@">SnpEff4.3</token>
18 <token name="@snpeff_database_url@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token> 18 <token name="@snpeff_database_url@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
19 <token name="@java_options@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token> 19 <token name="@java_options@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
20 <token name="@external_documentation@"> 20 <token name="@external_documentation@">
21 21
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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. 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.
36 36
37 **Pre-cached databases** 37 **Pre-cached databases**
38 38
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. 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... 41 In you *do not see them* keep reading...
42 42
43 **Download pre-built databases** 43 **Download pre-built databases**
44 44
46 46
47 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need. 47 #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need.
48 #. Use **SnpEff download** tool to download the database. 48 #. Use **SnpEff download** tool to download the database.
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. 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. 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.
52 52
53 **Create your own database** 53 **Create your own database**
54 54
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: 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:
56 56
57 #. Download Genbank record corresponding to your genome of interest from from NCBI. 57 #. Download Genbank record corresponding to your genome of interest from NCBI.
58 #. Use **SnpEff build** to create the database. 58 #. Use **SnpEff build** to create the database.
59 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter). 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. 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> 63 </token>
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