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@" > /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 <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: 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
