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 <dan@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/b9afd514145740b4d5999158...

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-inte...

(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/73bb36c4ee3b34c3ca32ed83...

any ideas?

Brad -- Brad Langhorst langhorst@neb.com

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-- Brad Langhorst langhorst@neb.com