comparison snpEff_macros.xml @ 31:b7029a54f73e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7

30:0c8a8cd9dd5b

<macros>
    <xml name="requirement">
        <requirement type="package" version="4.3.1t">snpeff</requirement>
        <yield/>
    </xml>
  <xml name="stdio">
    <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />

  <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>
  <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>

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.

31:b7029a54f73e

<macros>
    <xml name="requirement">
        <requirement type="package" version="5.2">snpeff</requirement>
        <yield/>
    </xml>
  <xml name="stdio">
    <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />

  <xml name="version_command">
    <version_command><![CDATA[
snpEff -version
    ]]></version_command>
  </xml>
  <token name="@WRAPPER_VERSION@">0</token>
  <token name="@SNPEFF_VERSION@">5.2</token>
  <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>

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.