annotate snpEff_macros.xml @ 30:c7275bd8b4d6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 280d5247becaa9a70db9c5c4a2f1fc50d302838a

<macros>
  <token name="@TOOL_VERSION@">5.2</token>
  <token name="@VERSION_SUFFIX@">0</token>
  <token name="@SNPEFF_VERSION@">SnpEff5.2</token>
  <xml name="requirement">
      <requirement type="package" version="@TOOL_VERSION@">snpeff</requirement>
      <yield/>
  </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="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
  <xml name="ref_select">
    <conditional name="reference_source">
        <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
            <option value="cached">Locally cached</option>
            <option value="history">History</option>
        </param>
        <when value="cached">
            <param name="ref_file" type="select" label="Select reference genome">
                <options from_data_table="fasta_indexes"/>
            </param>
        </when>
        <when value="history">
            <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/>
        </when>
    </conditional>
  </xml>
  <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 **SnpEff eff** tool.

In you *do not see them* keep reading...

**Download pre-built databases**

SnpEff project generates large numbers of pre-build databases. To obtain and use them 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>