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.
Alex,
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.
Finally, please always cc the mailing list for community and archival purposes.
Thanks, J.