For what it's worth (not much ;), I think the dataset naming is the single 
least intuitive part of the galaxy system for biologists.

I think there's a proposal to "fix" this problem - and mainain the connection 
between input data set and derived data, but It doesn't seem to have gone 
anywhere yet.

Anyway, you have to check the name of the field for each tool - it's sometimes 
"input" and sometimes something else.

You want to use the #{} for naming.  The ${} stuff is for parameters

I also do this kind of thing: to keep the names from getting too long.

#{input_1 | basename}.bam

The basename removes everything after the last . character.


From: <> 
on behalf of Jan Hapala <>
Sent: Wednesday, November 12, 2014 7:49 AM
To: galaxy-dev
Subject: [galaxy-dev] rename output dataset in workflow - input dataset variable


I want to rename ouput datasets in a workflow in such a way that the name 
contains the name of the input dataset. I could not find instructions in the 
manual (and this info is missing in the Workflow editor - would be really 
helpful there!).

I tried #{input}, e.g. "stats on: #{input}" (with no quotes), but I keep 
getting just "stats on:" The variable is empty. When I use ${input}, I get a 
variable field in the workflow form (I do not want this).

My G. instance: Galaxy changeset: 

Can anyone help me, please?
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