Problem fixed. I should do <command interpreter="perl">rpc_client.pl -u http://hiv-dev.lanl.gov:8081/tools/rpc -m formatconverter.convertFormat "sequencesText" "$sequence"</command> instead of <command interpreter="perl">perl rpc_client.pl -u http://hiv-dev.lanl.gov:8081/tools/rpc -m formatconverter.convertFormat "sequencesText" "$sequence"</command> Sorry for bothering.

Hi,

When I put the following in my tool xml <command>perl rpc_client.pl -u http://hiv-dev.lanl.gov:8081/tools/rpc -m formatconverter.convertFormat "sequencesText" "$sequence"</command>

And run the tool, it only execute " perl rpc_client.pl "sequencesText" "$sequence" ". Those options " -u http://hiv-dev.lanl.gov:8081/tools/rpc -m formatconverter.convertFormat " are ignored. How to fix this problem?

Thanks