Hi Dannon,

Sorry, I guess I still don't quite get it.  So I should keep the Input
Dataset name the default which is "Input Dataset".  In the next subsequent
step in the workflow I then edit step actions Rename Dataset/output_file
with "${Input Dataset} groomed", for example.  This gives me the same error
as before.  It is still unclear to me what the actual variable name is for
the input dataset so that I can use it to rename output in later steps.  Do
you have an example workflow that uses the input data set name to name the
output of downstream workflow steps that you could share with me as an
example so I can see the usage?  Even a simple two step workflow would do.

Thanks again,
Matt

On Wed, Apr 13, 2011 at 6:09 AM, Dannon Baker <dannonba...@me.com> wrote:

> The input dataset steps do not use workflow parameters as they don't
> actually create output datasets, but rather act as more of a temporary
> handle.  Remove the parameter tags from the input steps and just referring
> to those same parameter names in the subsequent steps you wanted to use them
> with should work and I think will allow you to do what you want.
>
> Thank you for pointing out the error though, this should definitely be more
> gracefully handled and supported with some help text in the editor, I'll see
> what I can do about that.  Let me know if this doesn't get up and running
> and I'll do what I can to help!
>
> -Dannon
>
>
>
>
> On 04/12/2011 06:20 PM, Matthew Conte wrote:
>
>> 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'
>> URL: http://localhost:8080/galaxy/workflow/run?id=f597429621d6eb2b
>> 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
>>
> \
>
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