Re: [galaxy-dev] generate dynamic select list based on other input dataset

2012-02-13 Thread Holger Klein 
Hi Jeremy,

I understood the  tags help if you want to filter input data
based on options in a .loc file, right?
My aim is to extract the column names of an input dataset, present them
in a selection box or dropdown list, let the user choose one, and
process the input set (with two inputs, the input set itself and the
selection made based on the input set).

Do you think that something like this is possible at all?

I attach the source of my dummy module and the python library which I
use via . The Syntax error I get is
SyntaxError: invalid syntax (, line 1)
The complete traceback is below.

The thread I was referring to in my mail can be found here:
http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03666.html
(Dec 12, 2011; Dynamic Tool Parameter Lists).

Cheers,
Holger




Module weberror.evalexception.middleware:364 in respond view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output view
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.tool_runner:68 in index view
>>  template, vars = tool.handle_input( trans, params.__dict__ )
Module galaxy.tools:1147 in handle_input view
>>  state = self.new_state( trans )
Module galaxy.tools:1075 in new_state view
>>  self.fill_in_new_state( trans, inputs, state.inputs )
Module galaxy.tools:1084 in fill_in_new_state view
>>  state[ input.name ] = input.get_initial_value( trans, context )
Module galaxy.tools.parameters.basic:788 in get_initial_value view
>>  options = list( self.get_options( trans, context ) )
Module galaxy.tools.parameters.basic:641 in get_options view
>>  return eval( self.dynamic_options, self.tool.code_namespace,
other_values )
SyntaxError: invalid syntax (, line 1)




On 02/13/2012 03:04 PM, Jeremy Goecks wrote:
> Holger,
> 
> Have you looked at how dynamic options work and whether they would be
> sufficient for your use? See the tag syntax for details:
> 
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.3E_tag_set
>  Syntax#A.3Cfilter.3E_tag_set>
> 
> To specifically address your problem: can you determine the particular
> place where the syntax error is appearing? And can you provide a link to
> the thread that you're using as a starting point?
> 
> Thanks,
> J.
> 
> 
> On Feb 10, 2012, at 3:43 PM, Holger Klein wrote:
> 
>> Dear all,
>>
>> I'm still stuck with the problem to dynamically generate an option list
>> extracted from a user-selectable input dataset. Does anybody have
>> experience here, or is this not possible at all?
>>
>> Have a nice weekend,
>> Holger
>>
>>
>> On 02/07/2012 09:58 PM, Holger Klein wrote:
>>> Dear all,
>>>
>>> I have a working module which generates wig files for genomic annotation
>>> from a single column of a bigger input data matrix (Input A). In the
>>> current state, the user has to input the column name (Input B) from
>>> which to calculate the values in the wig file.
>>>
>>> Now I'd like to modify the xml in such a way, that depending on the
>>> input dataset (Input A) a dynamic list for Input B is generated.
>>>
>>> I found Hans-Rudolf Hotz' hints from some time ago on this list and
>>> thought that the following would be a good start:
>>>
>>> >>   label  = "InputBName"
>>>   format = "data"
>>>   type   = "select"
>>>   help   = "Use tickboxes to select model"
>>>   display = "radio"
>>>   dynamic_options = "getInputBOptions($InputA)" />
>>>
>>> 
>>>
>>> getInputBOptionsFromInputA.py contains a single function
>>> def getInputBOptions($InputA):
>>>## parse Input A
>>>## create list InputBOptions
>>>return(InputBOptions)
>>>
>>> Using this approach I get an invalid syntax message when trying to even
>>> open the module - in any case I have the feeling that something is still
>>> missing here.
>>> Did anybody solve a similar problem already and could give me a hint on
>>> how to solve that?
>>>
>>> Cheers,
>>> Holger
>>>
>>>
>>>
>>>
>>
>>
>> -- 
>> Dr. Holger Klein
>> Core Facility Bioinformatics
>> Institute of Molecular Biology gGmbH (IMB)
>> http://www.imb-mainz.de/
>> Tel: +49(6131) 39 21511
>> ___
>> 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/
> 


-- 
Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Bio

Re: [galaxy-dev] generate dynamic select list based on other input dataset

2012-02-13 Thread Jeremy Goecks 
Holger,

Have you looked at how dynamic options work and whether they would be 
sufficient for your use? See the tag syntax for details:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.3E_tag_set

To specifically address your problem: can you determine the particular place 
where the syntax error is appearing? And can you provide a link to the thread 
that you're using as a starting point?

Thanks,
J.


On Feb 10, 2012, at 3:43 PM, Holger Klein wrote:

> Dear all,
> 
> I'm still stuck with the problem to dynamically generate an option list
> extracted from a user-selectable input dataset. Does anybody have
> experience here, or is this not possible at all?
> 
> Have a nice weekend,
> Holger
> 
> 
> On 02/07/2012 09:58 PM, Holger Klein wrote:
>> Dear all,
>> 
>> I have a working module which generates wig files for genomic annotation
>> from a single column of a bigger input data matrix (Input A). In the
>> current state, the user has to input the column name (Input B) from
>> which to calculate the values in the wig file.
>> 
>> Now I'd like to modify the xml in such a way, that depending on the
>> input dataset (Input A) a dynamic list for Input B is generated.
>> 
>> I found Hans-Rudolf Hotz' hints from some time ago on this list and
>> thought that the following would be a good start:
>> 
>> >   label  = "InputBName"
>>   format = "data"
>>   type   = "select"
>>   help   = "Use tickboxes to select model"
>>   display = "radio"
>>   dynamic_options = "getInputBOptions($InputA)" />
>> 
>> 
>> 
>> getInputBOptionsFromInputA.py contains a single function
>> def getInputBOptions($InputA):
>>## parse Input A
>>## create list InputBOptions
>>return(InputBOptions)
>> 
>> Using this approach I get an invalid syntax message when trying to even
>> open the module - in any case I have the feeling that something is still
>> missing here.
>> Did anybody solve a similar problem already and could give me a hint on
>> how to solve that?
>> 
>> Cheers,
>> Holger
>> 
>> 
>> 
>> 
> 
> 
> -- 
> Dr. Holger Klein
> Core Facility Bioinformatics
> Institute of Molecular Biology gGmbH (IMB)
> http://www.imb-mainz.de/
> Tel: +49(6131) 39 21511
> ___
> 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/

___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] generate dynamic select list based on other input dataset

2012-02-10 Thread Holger Klein 
Dear all,

I'm still stuck with the problem to dynamically generate an option list
extracted from a user-selectable input dataset. Does anybody have
experience here, or is this not possible at all?

Have a nice weekend,
Holger


On 02/07/2012 09:58 PM, Holger Klein wrote:
> Dear all,
> 
> I have a working module which generates wig files for genomic annotation
> from a single column of a bigger input data matrix (Input A). In the
> current state, the user has to input the column name (Input B) from
> which to calculate the values in the wig file.
> 
> Now I'd like to modify the xml in such a way, that depending on the
> input dataset (Input A) a dynamic list for Input B is generated.
> 
> I found Hans-Rudolf Hotz' hints from some time ago on this list and
> thought that the following would be a good start:
> 
> label  = "InputBName"
>format = "data"
>type   = "select"
>help   = "Use tickboxes to select model"
>display = "radio"
>dynamic_options = "getInputBOptions($InputA)" />
> 
> 
> 
> getInputBOptionsFromInputA.py contains a single function
> def getInputBOptions($InputA):
> ## parse Input A
> ## create list InputBOptions
> return(InputBOptions)
> 
> Using this approach I get an invalid syntax message when trying to even
> open the module - in any case I have the feeling that something is still
> missing here.
> Did anybody solve a similar problem already and could give me a hint on
> how to solve that?
> 
> Cheers,
> Holger
> 
> 
> 
> 


-- 
Dr. Holger Klein
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
http://www.imb-mainz.de/
Tel: +49(6131) 39 21511
___
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/