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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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