Hi Brad,

Thanks for reporting this issue. 

I have confirmed that there is an issue with workflow parameter substitution 
not working properly when inside of Grouping constructs (such as the paired 
end/single end conditional). We've opened a Trello card 
(https://trello.com/c/DvAea8kr) and Dannon, the developer of this feature, will 
work on a fix when he has a chance.


Thanks for using Galaxy,

Dan


On Mar 15, 2013, at 9:35 PM, Langhorst, Brad wrote:

> Hi Dan:
> I've transplanted that fix - looks good in workflow editing.
> When i try to run the workflow though, I get this stack  trace:
> 
> URL: http://galaxy.neb.com/workflow/run?id=b3c161103f7e2a00
> File 
> '/mnt/ngswork/galaxy/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 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
>  line 80 in __call__
>   return self.application(environ, start_response)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>  line 91 in __call__
>   return self.app( environ, start_response )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>  line 632 in __call__
>   return self.application(environ, start_response)
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
> 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
> 185 in handle_request
>   body = method( trans, **kwargs )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py',
>  line 1514 in run
>   enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults)
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
> line 848 in fill_template
>   return self.fill_template_mako( filename, **kwargs )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
> line 859 in fill_template_mako
>   return template.render( **data )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', 
> line 296 in render
>   return runtime._render(self, self.callable_, args, data)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', 
> line 660 in _render
>   **_kwargs_for_callable(callable_, data))
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', 
> line 692 in _render_context
>   _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', 
> line 718 in _exec_template
>   callable_(context, *args, **kwargs)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', 
> line 42 in render_body
>   __M_writer(unicode(next.body()))
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/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 
> '/mnt/ngswork/galaxy/galaxy-dist/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 
> '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py',
>  line 429 in render_do_inputs
>   __M_writer(unicode(do_inputs( input.cases[ current_case ].inputs, 
> group_values, group_errors, new_prefix, step, other_values, already_used )))
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py',
>  line 340 in do_inputs
>   return 
> render_do_inputs(context,inputs,values,errors,prefix,step,other_values,already_used)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/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 
> '/mnt/ngswork/galaxy/galaxy-dist/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 
> '/mnt/ngswork/galaxy/galaxy-dist/database/compiled_templates/workflow/run.mako.py',
>  line 571 in render_row_for_param
>   p_text = p_text.replace(rematch, '<span style="background-color:%s" 
> class="wfpspan wf_parm__%s">%s</span>' % (wf_parms[rematch[2:-1]], 
> rematch[2:-1], rematch[2:-1]))
> KeyError: 'min_insert'
> 
> 
> I'll hack a bit on it to see why min_insert is not in wf_params...
> 
> 
> Brad
> On Mar 15, 2013, at 5:28 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> 
>> Hi Brad,
>> 
>> Thanks for reporting this issue. It has been fixed in -central and will be 
>> available in the next stable release: 
>> https://bitbucket.org/galaxy/galaxy-central/commits/b9afd514145740b4d5999158d51bd7dc4a409a99
>> 
>> 
>> Thanks for using Galaxy,
>> 
>> Dan
>> 
>> 
>> On Mar 15, 2013, at 5:04 PM, Langhorst, Brad wrote:
>> 
>>> Workflow parameters still seem to be broken for me.
>>> 
>>> I'm seeing the same problem as Liisa Koski
>>> http://dev.list.galaxyproject.org/Can-t-specify-workflow-parameters-for-integer-values-td4658193.html
>>> 
>>> (this message comes up when i edit a workflow with ${mininsert} set on a 
>>> bowtie2 job)
>>> 
>>> Problems were encountered loading this workflow (possibly a result of tool 
>>> upgrades). Please review the following parameters and then save.
>>> Step 9: Bowtie2
>>> Value no longer valid for 'Minimum insert size for valid paired-end 
>>> alignments', replaced with default
>>> 
>>> 
>>> but Im running a release release_2013.02.08
>>> and I've verified that this commit is present in the running code
>>> 
>>> https://bitbucket.org/galaxy/galaxy-central/commits/73bb36c4ee3b34c3ca32ed830b4f91df79b971c5
>>> 
>>> any ideas?
>>> 
>>> 
>>> 
>>> Brad
>>> --
>>> Brad Langhorst
>>> langho...@neb.com
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___________________________________________________________
>>> 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/
>> 
> 
> --
> Brad Langhorst
> langho...@neb.com
> 
> 
> 
> 
> 

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