Mercurial > repos > iuc > snpeff
view snpEff_macros.xml @ 20:8f92c2b26e6d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
author | iuc |
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date | Fri, 25 Jan 2019 12:29:48 -0500 |
parents | 65ae79bddc69 |
children | 74aebe30fb52 |
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<macros> <xml name="requirement"> <requirement type="package" version="4.3.1t">snpeff</requirement> </xml> <xml name="stdio"> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> <xml name="version_command"> <version_command><![CDATA[ snpEff -version ]]></version_command> </xml> <token name="@WRAPPER_VERSION@">4.3+T</token> <token name="@SNPEFF_VERSION@">SnpEff4.3</token> <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token> <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token> <token name="@EXTERNAL_DOCUMENTATION@"> ------- To learn more about snpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html </token> <token name="@SNPEFF_IN_GALAXY_INFO@"> ------- .. class:: warningmark **Using SnpEff in Galaxy: A few points to remember** 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. **Pre-cached databases** 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. In you *do not see them* keep reading... **Download pre-built databases** SnpEff project generates large numbers of pre-build databases. These are available at @SNPEFF_DATABASE_URL@ and can downloaded. Follow these steps: #. Use **SnpEff databases** tool to generate a list of existing databases. Note the name of the database you need. #. Use **SnpEff download** tool to download the database. #. 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. 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. **Create your own database** 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: #. 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. #. Use **SnpEff build** to create the database. #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter). 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. </token> <xml name="citations"> <citations> <citation type="doi">10.4161/fly.19695</citation> <yield /> </citations> </xml> </macros>