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.

On Nov 28, 2011, at 12:21 PM, Aurélien Bernard wrote:

> Hi everybody,
> 
> 
> I'm currently trying to create a wrapper for one of my program.
> 
> This program generates several output file and the name of each output file 
> is derived from the name of the main input file.
> 
> 
> In the .xml file I try to get my output files with the following tag:
> 
> <outputs>
>     <data from_work_dir="${input_file}.out" label="${input_file} main output" 
> format="txt" />
>     ...
> </outputs>
> 
> The corresponding input file tag:
> 
> <param name="input_file" type="data" label="Input label" format="alr" 
> help="Requested file type: ALR" />
> 
> 
> The problem is that the content of the "from_work_dir" attribute is not 
> interpreted by galaxy (Contrary to the label attribute) and therefore I get 
> this error message:
> 
> galaxy.jobs DEBUG 2011-11-28 17:44:24,431 finish(): Could not move 
> /home/galaxy/galaxy-dist/database/job_working_directory/326/${input_file}.out 
> to /home/galaxy/galaxy-dist/database/files/000/dataset_684.dat as directed by 
> from_work_dir
> 
> Do I made a syntax error ? Do I misunderstand the function of the 
> from_work_dir attribute ?
> 
> 
> Thank you in advance for your help.
> 
> Best regards,
> 
> 
> Aurélien Bernard
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