comparison snpEff_macros.xml @ 4:698ef30638a8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d

3:b24873564cf6

    <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>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>
  <token name="@CITATION_SECTION@">------

**Citation**

For the underlying tool, please cite the following two publications:

SnpEff citation:
"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly 6(2):80-92, 2012

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

4:698ef30638a8

    <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>