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>