Re: [galaxy-dev] Output file naming / dataset's label

[Dannon Baker]

Ahh, I understand your confusion now.  The previous bit you pointed out 
was an error indeed, but not the one you were running into.  The 
variable name should be whatever you want it to be, it doesn't have to 
map to an existing value like "Input Dataset", but there's an issue with 
the way the tags are handled for parameter replacement that causes a 
failure when the name contains spaces.  Instead of ${Input Dataset}, try 
${input_dataset}.  I have a fix for this that should be available in the 
near future, as part of a larger set of changes that should make 
parameters much more accessible.


On 04/13/2011 10:11 AM, Matthew Conte wrote:
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

\


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/