I am really very sorry about that. It seems this must be related to my
pull request "fixing" multiple input tool parameters. I have spent
some time this morning trying to reproduce your error, but I cannot.
That said I think I can fix it, this patch should work:

diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako
index c7cd138..175f148 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -243,9 +243,12 @@ if wf_parms:
             %if isinstance( param, DataToolParameter ):
                 %if ( prefix + param.name ) in step.input_connections_by_name:
                     <%
-                        conn = step.input_connections_by_name[ prefix
+ param.name ]
+                        conns = step.input_connections_by_name[
prefix + param.name ]
+                        if not isinstance(conns, list):
+                            conns = [conns]
+                        vals = ["Output dataset '%s' from step %d" %
(conn.output_name, int(conn.output_step.order_index)+1
                     %>
-                    Output dataset '${conn.output_name}' from step
${int(conn.output_step.order_index)+1}
+                    ${",".join(vals)}
                 %else:
                     ## FIXME: Initialize in the controller
                     <%

Can you apply the patch and tell me if it works? Probably a similar
fix needs to be applied to display.mako also, but I want to be able to
recreate the problem first or at least verify this fixes it.

-John

On Mon, Dec 3, 2012 at 4:45 AM, Marc Logghe <marc.log...@ablynx.com> wrote:
> Hi,
>
> I have a workflow that basically needs a select parameter as input. 2 steps
> in the workflow actually need the very same input. I don’t think there is a
> (easy) way to let the user only input the parameter once and that it is
> passed to both steps.
>
> Anyhow, currently - as a workaround and not very user friendly - the user
> needs to input the very same parameter twice, for each step where that
> parameter is required.
>
> The first issue however, is that as soon as the first parameter is set, the
> second is set as well apparently (they have the same name, that could
> explain) which is fine, but not to the chosen one, eg. both are kind of
> reset to default. No errors or something, simply reset, which makes it
> impossible to enter the parameter.
>
>
>
> Next, I hoped to solve the issue by upgrading galaxy to the most recent
> version. This was not the case since the workflow did not run at all
> anymore, which brings me to the second issue (see exception dump below).
>
> Any ideas anyone ?
>
> Thanks and regards,
>
> Marc
>
>
>
>
>
> Error - <type 'exceptions.AttributeError'>: 'list' object has no attribute
> 'output_name'
>
> URL: http://smith:8889/workflow/run?id=4b187121143038ff
>
> File
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py',
> line 143 in __call__
>
>   app_iter = self.application(environ, start_response)
>
> File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
> line 80 in __call__
>
>   return self.application(environ, start_response)
>
> File
> '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
> line 632 in __call__
>
>   return self.application(environ, start_response)
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in
> __call__
>
>   body = method( trans, **kwargs )
>
> File
> '/home/galaxy/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/workflow.py',
> line 1523 in run
>
>   enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults)
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line
> 836 in fill_template
>
>   return self.fill_template_mako( filename, **kwargs )
>
> File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line
> 847 in fill_template_mako
>
>   return template.render( **data )
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
> line 296 in render
>
>   return runtime._render(self, self.callable_, args, data)
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
> line 660 in _render
>
>   **_kwargs_for_callable(callable_, data))
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
> line 692 in _render_context
>
>   _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
>
> File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
> line 718 in _exec_template
>
>   callable_(context, *args, **kwargs)
>
> File '/home/galaxy/galaxy-dev/database/compiled_templates/base.mako.py',
> line 42 in render_body
>
>   __M_writer(unicode(next.body()))
>
> File
> '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py',
> line 171 in render_body
>
>   __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get(
> step.id, dict() ), "", step, None, used_accumulator )))
>
> File
> '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py',
> line 40 in do_inputs
>
>   return
> render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values,already_used)
>
> File
> '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py',
> line 435 in render_do_inputs
>
>   __M_writer(unicode(row_for_param( input, values[ input.name ],
> other_values, errors, prefix, step, already_used )))
>
> File
> '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py',
> line 338 in row_for_param
>
>   return
> render_row_for_param(context,param,value,other_values,error_dict,prefix,step,already_used)
>
> File
> '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py',
> line 498 in render_row_for_param
>
>   __M_writer(unicode(conn.output_name))
>
> AttributeError: 'list' object has no attribute 'output_name'
>
>
>
>
>
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