view snpEff_macros.xml @ 6:20f0429a4bfe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="4.1">snpEff</requirement>
        </requirements>
    </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>
  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
  <xml name="version_command">
    <version_command><![CDATA[
    if [ -z "$SNPEFF_JAR_PATH" ]; then
        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
    ]]></version_command>
  </xml>
  <token name="@WRAPPER_VERSION@">4.1</token>
  <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
  <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token>
  <token name="@EXTERNAL_DOCUMENTATION@">

For details about this tool, please go to:
	http://snpeff.sourceforge.net/SnpEff_manual.html

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