annotate snpSift_macros.xml @ 2:a7cbaf3beadd draft default tip

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

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="4.1">snpsift</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_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
  <xml name="version_command">
    <version_command><![CDATA[
    if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
    java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
    ]]></version_command>
  </xml>
  <token name="@WRAPPER_VERSION@">4.1</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">10.3389/fgene.2012.00035</citation>
        <yield />
      </citations>
  </xml>
</macros>