annotate snpEff_macros.xml @ 17:65ae79bddc69 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5ab504d384299d8c2ed496650f1f9e4a887cd102

<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>