Question: Adding custom tools: newbie
0
plindenbaum • 90 wrote:
Hi all, I'm learning how to create wrap a java program in my galaxy instance:
<?xml version="1.0"?>
<tool id="my_id" name="my_app" version="my_version" hidden="false">
<description>My tool</description>
<command interpreter="bash">/usr/bin/java -cp /var/lib1.jar:/var/lib2.jar tool.MyApp -n ${number} ${input} > ${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>blablabala</help>
</tool>
Questions:
1) the following xml raises an error in galaxy: (why)
/usr/bin/java : cannot execute binary file
2) where can I find the documentation about defining a global variable/parameter to replace :
/var/lib1.jar:/var/lib2.jar
with
${myclasspath}
3) if I fix an error in my tool.xml, do I have to restart my instance of galaxy ?
4) are XML-inclusions (x:include) supported by the XML processing of tools.xml ?
Thank you
Pierre
