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comparison snpEff_macros.xml @ 10:5b4ac70948d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef
author iuc
date Tue, 27 Mar 2018 09:44:18 -0400
parents 68693743661e
children 5a29ab10dba6
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equal deleted inserted replaced
9:68693743661e 10:5b4ac70948d2
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirement">
3 <requirements> 3 <requirement type="package" version="4.3.1t">snpeff</requirement>
4 <requirement type="package" version="4.3.1r">snpeff</requirement>
5 </requirements>
6 </xml> 4 </xml>
7 <xml name="stdio"> 5 <xml name="stdio">
8 <stdio> 6 <stdio>
9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
10 <exit_code range="1:" level="fatal" description="Error" /> 8 <exit_code range="1:" level="fatal" description="Error" />
13 <xml name="version_command"> 11 <xml name="version_command">
14 <version_command><![CDATA[ 12 <version_command><![CDATA[
15 snpEff -version 13 snpEff -version
16 ]]></version_command> 14 ]]></version_command>
17 </xml> 15 </xml>
18 <token name="@WRAPPER_VERSION@">4.3r</token> 16 <token name="@wrapper_version@">4.3.1t</token>
19 <token name="@SNPEFF_VERSION@">SnpEff4.3</token> 17 <token name="@snpeff_version@">SnpEff4.3</token>
20 <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>
21 <token name="@EXTERNAL_DOCUMENTATION@"> 19 <token name="@java_options@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
22 For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html 20 <token name="@external_documentation@">
21
22
23 -------
24
25 To learn more about snpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html
23 </token> 26 </token>
27 <token name="@snpeff_in_galaxy_info@">
28
29 -------
30
31 .. class:: warningmark
32
33 **Using SnpEff in Galaxy: A few points to remember**
34
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
37 **Pre-cached databases**
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.
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41 In you *do not see them* keep reading...
42
43 **Download pre-built databases**
44
45 SnpEff project generates large numbers of pre-build databases. These are available at @SNPEFF_DATABASE_URL@ and can downloaded. Follow these steps:
46
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.
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.
50
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
53 **Create your own database**
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:
56
57 #. Download Genbank record corresponding to your genome of interest from from NCBI.
58 #. Use **SnpEff build** to create the database.
59 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).
60
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.
62
63 </token>
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24 <xml name="citations"> 67 <xml name="citations">
25 <citations> 68 <citations>
26 <citation type="doi">10.4161/fly.19695</citation> 69 <citation type="doi">10.4161/fly.19695</citation>
27 <yield /> 70 <yield />
28 </citations> 71 </citations>