On Mon, May 19, 2014 at 9:29 AM, Pierre Lindenbaum
<pierre.lindenbaum(a)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@" > /tmp/galaxy.txt &&
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> /dev/null
> ${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 <nate(a)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:
https://twitter.com/jmchilton/status/468381976911556608
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.
Regards,
Peter