view snpEff_macros.xml @ 0:2a3a00c1fa0a draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e6d1b32be9df14beb1e2859a0d2fa29a2d09227e"

<macros>
    <xml name="requirement">
        <requirement type="package" version="4.5covid19">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="@WRAPPER_VERSION@">4.5covid19</token>
  <token name="@SNPEFF_VERSION@">SnpEff4.5</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

**Databases in the SnpEff Covid-19 edition**

This special version of SnpEff provides only a fixed number of
SARS-CoV-2-related genome databases.

Unlike with regular SnpEff releases, it is not possible to extend this set,
*i.e*, you cannot download additional databases or build custom databases for
this edition.
</token>



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