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 \