On Mon, May 19, 2014 at 9:29 AM, Pierre Lindenbaum
<pierre.lindenb...@univ-nantes.fr> wrote:
> This question was cross-posted on https://biostar.usegalaxy.org/p/7619/
> "Adding custom tools: resolving (external ) XML entities"
> I'd like to replace fragments of XML code in my custom tool declaration.
> My first idea was to use XML entities but it seems that the XML engine
> doesn't resolve them.
> (BTW: I know I can replace/declare things in $PATH and tool_dependencies.xml
> )
> Another idea was to use <macros><token...> but I cannot make it work  (see
> https://gist.github.com/lindenb/b2a04e0fefd4d295dba9 )
> my macros definition:
> <?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> my tool definition: as a test, I echoed the value of @JAVA_EXE@ in
> /tmp/galaxy.txt (the macro was *not replaced* )
> <?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}
> /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> the output of 'hg tip'
> changeset: 9312:788cd3d06541
> tag: tip
> parent: 9310:19f6e62bd372
> parent: 9311:d7f37a2fe690
> user: Nate Coraor <n...@bx.psu.edu>
> date: Mon Apr 08 12:30:08 2013 -0400
> summary: Merged stable. what's wrong in my <macros> definition ? Thanks.
> Pierre

Pierre - can you update to the current stable release and retest?

John suggested on Twitter that your Galaxy might be too old and perhaps
pre-dates the macro support:


That seems to fit - you appear to have a Galaxy from April 2013. We started
using the XML macros for the NCBI BLAST+ wrappers in August 2013, so
even if they were only on the development branch (galaxy-central) at that
point, they would surely have been in the stable branch (galaxy-dist) by
the close of 2013.



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