I'd like to do the same thing that Tanguy described. I'm trying to figure out the syntax to this within the workflow editor, but can't quite get it right. In your example Dannon, would you just set ${dataset_name} as the "Name" for your "Input dataset" to capture the input dataset name as a variable? When I do that and then try to run the workflow I get the following error:
Error - <type 'exceptions.KeyError'>: 'dataset_name'
File '/path-to-galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__
app_iter = self.application(environ, start_response)
File '/path-to-galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__
return self.application(environ, start_response)
File '/path-to-galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__
return self.application(environ, start_response)
File '/path-to-galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__
body = method( trans, **kwargs )
File '/path-to-galaxy-dist/lib/galaxy/web/controllers/workflow.py', line 1397 in run
incoming=kwargs )
File '/path-to-galaxy-dist/lib/galaxy/web/framework/__init__.py', line 650 in fill_template
return self.fill_template_mako( filename, **kwargs )
File '/path-to-galaxy-dist/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako
return template.render( **data )
File '/path-to-galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render
return runtime._render(self, self.callable_, args, data)
File '/path-to-galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render
_render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data))
File '/path-to-galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File '/path-to-galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template
callable_(context, *args, **kwargs)
File '/path-to-galaxy-dist/database/compiled_templates/
base.mako.py', line 40 in render_body
__M_writer(unicode(next.body()))
File '/path-to-galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda>
return lambda *args, **kwargs:callable_(self.context, *args, **kwargs)
File '/path-to-galaxy-dist/database/compiled_templates/workflow/
run.mako.py', line 172 in render_body
pja_ss = pja_ss.replace(rematch, '<span style="background-color:%s" class="wfpspan wf_parm__%s pja_wfp">%s</span>' % (wf_parms[rematch[2:-1]], rematch[2:-1], rematch[2:-1]))
KeyError: 'dataset_name'
Perhaps I'm missing something obvious?
Thanks,
Matt
On Wed, Dec 8, 2010 at 9:38 AM, Dannon Baker
<dannonbaker@me.com> wrote:
Tanguy,
My apologies for the delay in response. For now, the best way to do something like this would be to add rename dataset actions to each step where you want to modify the dataset name. You can do this within the workflow editor, in the right panel under "Edit Step Actions".
A new feature we've been working on will allow you to use variables within the rename action, among other places. Depending on how often you reuse workflows, it could save you a lot of time renaming things. An example would look something like this, for a rename dataset action: "Filtering ${dataset_name} on col2 > ${threshold}", where ${dataset_name} and ${threshold} are variables that are set when you run a workflow. These variables get replaced anywhere they are seen in the workflow tool parameters and step actions. This feature is not available yet, but we do expect it to be ready soon.
Thanks for using Galaxy,
Dannon
On Oct 28, 2010, at 4:40 AM, Tanguy Le Carrour wrote:
> Dear Galaxy Team,
>
> I started using Galaxy few months ago. I'm now setting up my first "real" workflows.
> I would like to keep the name of my input file through the various steps as dataset's label, maybe also modify it a bit, and finally give a "proper" name to the result file downloaded.
>
> A simple example:
> 1) date-sample_name.gff3 --[step1]-> date-sample_name-step1.tsv
> 2) date-sample_name-step1.tsv --[step2]-> date-sample_name-step1-step2.txt
> 3 download date-sample_name-step1-step2.txt
>
> I've seen that I can use the 'label' attribute in the tool config "data" tag to do so. But I don't know how to access the ${input.label} (?) and how to modify it.
>
> I doesn't stop me using my workflows, but it would definitely help my users not to get lost when they use them.
>
> Best regards,
> Tanguy Le Carrour
>
> --
> Tanguy LE CARROUR
>
> Functional Genomics Center Zurich
> ETH Zurich / University of Zurich
> Winterthurerstrasse 190
> 8057 Zurich
> Switzerland
>
>
>
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