On Thu, Feb 26, 2015 at 2:43 PM, John Chilton <jmchilton@gmail.com> wrote:
Also not need to escape $__tool_directory__ (so use $__tool_directory__ instead of \$__tool_directory__).
-John
If this was unclear, $VAR in the <command> XML fragment is taken to be a Python variable available within the Cheetah parser. Typically this would be one of your usr-set parameters. Escaping the dollar as \$VAR in the XML fragment means it is ignored by the Cheetah parser and becomes $VAR in the command line string, meaning an environment variable. Using bash syntax you can insert a default value, e.g. many tools use something like -t "\${GALAXY_SLOTS:-8}" which would default to 8 threads even in older Galaxy instances where the $GALAXY_SLOTS environment variable wasn't setup. Peter