view snpEff_macros.xml @ 10:5b4ac70948d2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit eea43430ff90fe6b13b295f6d5efb2208401a7ef

<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@">4.3.1t</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@">

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.. 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 from NCBI. 
 #. 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 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. 

</token>



  <xml name="citations">
      <citations>
        <citation type="doi">10.4161/fly.19695</citation>
        <yield />
      </citations>
  </xml>
</macros>