On 02/26/2015 03:43 PM, John Chilton wrote:
Sorry I wasn't clear about that - it hasn't reached galaxy-dist yet -
you can download the latest snapshot of 15.03 release (I believe it is
running on usegalaxy.org as of yesterday) via this link instead
https://bitbucket.org/galaxy/galaxy-central/get/release_15.03.zip.

Also not need to escape $__tool_directory__  (so use
$__tool_directory__ instead of \$__tool_directory__).

-John


thank you for your help John & Peter

hum... is there anything new with this version about tool.xml ?. I can see my tool in the right menu but the main page is blank (no input fields)

   127.0.0.1 - - [26/Feb/2015:16:09:07 +0200] "GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1" 200 - "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0"
   127.0.0.1 - - [26/Feb/2015:16:09:17 +0200] "GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1" 200 - "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0"
   127.0.0.1 - - [26/Feb/2015:16:09:27 +0200] "GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1" 200 - "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0"
   127.0.0.1 - - [26/Feb/2015:16:09:28 +0200] "GET
   /tool_runner?tool_id=com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS
   HTTP/1.1" 200 - "http://127.0.0.1:8080/"; "Mozilla/5.0 (X11; Ubuntu;
   Linux i686; rv:35.0) Gecko/20100101 Firefox/35.0"


$ xmllint --format tools/jvarkit2/vcffilterjs.xml
<?xml version="1.0"?>
<tool hidden="false" id="com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS" version="1.0.0" name="vcffilterjs">
  <requirements>
    <requirement type="binary">java</requirement>
  </requirements>
<command><![CDATA[echo "dir=$__tool_directory__ ." > /tmp/error7.txt && java -cp $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.129.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcffilterjs.jar com.github.lindenb.jvarkit.tools.vcffilterjs.VCFFilterJS -e '${expression}' -o ${output} ${input} 2>> /tmp/error7.txt ]]></command>
  <inputs>
    <param format="vcf" name="input" type="data" label="VCF input"/>
    <param name="expression" type="text" label="javascript expression">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
        </valid>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="vcf" name="output"/>
  </outputs>
  <stdio>
    <exit_code range="1:"/>
    <exit_code range=":-1"/>
  </stdio>
  <help>Help</help>
</tool>

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