discussion for https://biostar.usegalaxy.org/p/7619

galaxy.txt

@JAVA_EXE@

jvarkit_macros.xml

<?xml version="1.0"?>
<macros>
  <token name="@JAVA_EXE@">/usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java</token>
  <token name="@JVM_OPTIONS@">-Xmx500m</token>
</macros>

vcfhead.xml

<?xml version="1.0" encoding="UTF-8"?>
<tool id="com_github_lindenb_jvarkit_tools_misc_VcfHead" name="VcfHead" version="e098748b85acd5158a1ce612bd3d46e60948b9db" hidden="false">
  <description>Print the first lines of a VCF</description>
  <macros>
    <import>jvarkit_macros.xml</import>
  </macros>
  <command>echo "@JAVA_EXE@" &gt; /tmp/galaxy.txt &amp;&amp; zcat -f ${input} | @JAVA_EXE@ @JVM_OPTIONS@ -cp /commun/data/packages/htsjdk/dist/apache-ant-1.8.2-bzip2.jar:/commun/data/packages/htsjdk/dist/htsjdk-1.112.jar:/commun/data/packages/htsjdk/dist/commons-jexl-2.1.1.jar:/commun/data/packages/htsjdk/dist/commons-logging-1.1.1.jar:/commun/data/packages/jvarkit-git/vcfhead.jar com.github.lindenb.jvarkit.tools.misc.VcfHead  -n ${number} 2&gt; /dev/null &gt; ${output}</command>
  <inputs>
    <param format="vcf" name="input" type="data" label="Source VCF" optional="false"/>
    <param name="number" type="integer" value="10" label="Number of rows" optional="true"/>
  </inputs>
  <outputs>
    <data format="input" name="output" metadata_source="input"/>
  </outputs>
  <help>see https://github.com/lindenb/jvarkit/wiki/VcfHead</help>
</tool>

version.txt

$ hg tip
changeset:   9312:788cd3d06541
tag:         tip
parent:      9310:19f6e62bd372
parent:      9311:d7f37a2fe690
user:        Nate Coraor <nate@bx.psu.edu>
date:        Mon Apr 08 12:30:08 2013 -0400
summary:     Merged stable.