>> The particular behavior that you need isn't currently supported because the
>> value of from_work_dir isn't treated as a template. To work around this
>> limitation, you can do the move/copy operations in your tool wrapper; see
>> the wrappers for Bowtie and Sicer for examples on how to do this.
>> Good luck,
> Hi Jeremy,
> Is it possible to build the required string elsewhere in the .xml file using
> cheetah and then pass the resulting string like from_work_dir=$result or is
> using a wrapper really the only way to go? I'm writing a config for a tool
> that names the output files using the options, so I could potentially
> concatenate the option values to get the required file name if I could do
The best approach is for your tool to accept output file names; then, in the
command_line tag of the tool wrapper XML, you can build the output name based
on options chosen by the user.
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