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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