I don't think there is a way given the implementation. The name of the association is repeatname_0|input1 but the | is treated as a special symbol so it won't be used to get the parameter.
I have opened a PR to allow this:
https://github.com/galaxyproject/galaxy/pull/662
The syntax in the above example would be something like #{repeatname_0.input1 | basename}.bam after that pull request.
-John
On Tue, Jul 28, 2015 at 2:47 PM, Nicolas Lapalu nicolas.lapalu@versailles.inra.fr wrote:
Hi all,
An old question without reply. Is there a solution to this problem ? Thanks for your help.
nico
Le 18/07/2014 12:51, Ulf Schaefer a écrit :
Hi all
We frequently use the syntax below to rename outputs of workflows that we run in batch. It is convenient to have sample names from fastqs carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g. the VelvetOptimiser. Does anybody know if there is a syntax to make this work, maybe
#{repeatname[0].input1 | basename}.bam ?
Thanks a lot for your help Ulf
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