Thanks, but ${foo.name} did not work in the workflow to rename an output file. It takes ${foo.name} to be a user provided parameter.

${foo.name} will definitely work in tool definitions, but that means I have to change ALL the default tool names for all the tool in galaxy...Surely there must be a way to rename an output file to the original input file in the workflow step "Rename Dataset"? 

Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru
+1-650-799-6839




On Dec 31, 2011, at 4:17 PM, Peter Cock wrote:

On Sat, Dec 31, 2011 at 11:43 PM, Thon deBoer <thondeboer@me.com> wrote:
I digged some more and I guess I could use the rename dataset option in a
workflow, but I can't find how I can rename a dataset using the original
input name.
I tried to use the same notation as those used in the tools (such as
${input.name}) but that just treats the input.name as a user provided
parameter, which is NOT my intention.

Is there any way I can rename a dataset using information from the orginal
input dataset name? It seems a trivially obvious thing to be able to do, but
I can't figure it out...Hopefully this is just an oversight on my part!


From memory, if the input file parameter is called foo, you can
use ${foo.name}, and there is also something called $on_string
used in an example here:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

Peter