On Thu, Feb 26, 2015 at 2:43 PM, John Chilton <jmchil...@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
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