>> Aurelien,
>> 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,
>> J.
> 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 
> that. 


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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