Dear Galaxy team,

i tried to run the varscan somatic tool from fcaramia on two pileup files
but i got the following error:
Unknown Input: COMMAND::java -jar

The command was the following:
Job Command-Line:    perl /home/karin/shed_tools/
"COMMAND::java -jar $JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic"
"OPTION::--min-coverage 8" "OPTION::--min-coverage-normal 8"
"OPTION::--min-coverage-tumor 8" "OPTION::--min-var-freq 0.1"
"OPTION::--min-freq-for-hom 0.75" "OPTION::--normal-purity 1.0"
"OPTION::--tumor-purity 1.0" "OPTION::--p-value 0.99"
"OPTION::--somatic-p-value 0.05" "OPTION::--strand-filter 1"
"OPTION::--validation 0" "OPTION::--output-vcf 1"

I also tried to change the varscan_somatic.xml file in such a way that i
removed the "COMMAND::" tags etc. and used it without the
file. After doing that, the tool ran without errors but i obtained empty
files. Redoing the same command on my local computer ran properly and i
obtained the wanted outputs:

java -jar $JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic
/home/karin/galaxy-dist/database/files/000/dataset_109.dat dataset_131.dat
--output-snp dataset_131.dat --output-indel dataset_132.dat
--min-coverage 8 --min-coverage-normal 8 --min-coverage-tumor 8
--min-var-freq 0.1 --min-freq-for-hom 0.75 --normal-purity 1.0
--tumor-purity 1.0 --p-value 0.99 --somatic-p-value 0.05 --strand-filter 1
2> testlog

in dataset_131.dat the snps, indels: dataset_132.dat, and some information
(varscan directs this info on stderr) in testlog.

Any idea how to fix that? i appreciate any information on how this may be

Thanks a lot and best wishes,
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