comparison snpEff_macros.xml @ 7:7adfd0589f49 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1

6:20f0429a4bfe

<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 />

7:7adfd0589f49

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="4.3k">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>
  <xml name="version_command">
    <version_command><![CDATA[
snpEff -version
    ]]></version_command>
  </xml>
  <token name="@WRAPPER_VERSION@">4.3k</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="@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 />