Re: [galaxy-dev] Multiple output tools in Workflow

[Peter Cock]

On Thu, Jul 17, 2014 at 2:43 PM, Calogero Zarbo  wrote:
> Ok, thanks for the the tip.
>
> I changed the XML to this one:
>
>
> 
>  label="Training Dataset extracted from ${input_dataset.name}">
> 
> format="fbk-svm-dataset"/>
> 
>
>
> 
>  label="Validation Dataset extracted from ${input_dataset.name}">
> 
> format="fbk-svm-dataset"/>
> 
>
>
> 
>
> 
> format_condition['format_options']  == "fbk"
> 
>
> 
> format_condition['format_options']  == "fbk"
> 
>
> 
>
> Still is not working, maybe the " format="fbk-svm-dataset"/>" . Maybe it has some problem since the
> "format_options" parameter is inside a "conditional" tag?
>
> Thanks a lot for your time.

I'm not sure off hand - is your complete wrapper in a public repository
somewhere we can look at? However, my general advice would be:

First of all, get it working in the normal tool usage mode (tested by hand).

Then I would get it working with functional tests.

Finally I would test it by hand in the workflow editor, at which point any
problem is probably Galaxy's fault ;)

Peter
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Re: [galaxy-dev] Multiple output tools in Workflow

[Calogero Zarbo]

Ok, thanks for the the tip.

I changed the XML to this one:




   





   





format_condition['format_options']  == "fbk"



format_condition['format_options']  == "fbk"




Still is not working, maybe the "" . Maybe it has some problem since the
"format_options" parameter is inside a "conditional" tag?

Thanks a lot for your time.



On Thu, Jul 17, 2014 at 3:08 PM, Peter Cock 
wrote:

> On Thu, Jul 17, 2014 at 1:58 PM, Calogero Zarbo  wrote:
> > Hello Peter,
> >
> > Thanks for your answer.
> >
> > I tried your come but I am still not able to make it work the way I want.
> > I mean that in the workflow design page, when I switch the parameter, it
> > doesn't change the graphical list of outputs of the tool. How can I fix
> it?
> > I want something like the Input, where it shows different outputs
> according
> > to the selected parameter from the select.
> >
> > Here is the XML code:
> >
> >
> > 
> > 
> >
> > 
> >
> > 
> > FBK Format
> > ShoweLab
> > Format
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> >
> > 
> > 
> >  > label="Training Dataset extracted from ${input_dataset.name}">
> > format_condition["format_options"] ==
> > "showelab"
> >
> > 
> >  > label="Validation Dataset extracted from ${input_dataset.name}">
> > format_condition["format_options"] ==
> > "showelab"
> >
> > 
> >  > label="Training Dataset extracted from ${input_dataset.name}">
> > format_condition["format_options"]  == "fbk"
> >
> > 
> > 
> > format_condition["format_options"]  == "fbk"
> >
> > 
> >  > label="Validation Dataset extracted from ${input_dataset.name}">
> > format_condition["format_options"]  == "fbk"
> >
> > 
> >  label="Validation
> > Dataset Labels extracted from ${input_fbk_dataset_labels.name}">
> > format_condition["format_options"]  == "fbk"
> > 
> > 
>
> You appear to have multiple defined datasets (three versions of
> trainingDataset) which may be the problem, as the name is meant
> to be unique.
>
> I think you should have ONE  tag for trainingDataset but
> set this up to switch output formats accordingly.
>
> Peter
>



-- 
Calogero Zarbo


FBK - Fondazione Bruno Kessler
Center for Information Technology
Mpba - Predictive Models for Biomedicine & Environment
Via Sommarive, 18- 38123 Povo (Trento) IT
e-mail: za...@fbk.eu

phone: +39 0461 314 674
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Re: [galaxy-dev] Multiple output tools in Workflow

[Peter Cock]

On Thu, Jul 17, 2014 at 1:58 PM, Calogero Zarbo  wrote:
> Hello Peter,
>
> Thanks for your answer.
>
> I tried your come but I am still not able to make it work the way I want.
> I mean that in the workflow design page, when I switch the parameter, it
> doesn't change the graphical list of outputs of the tool. How can I fix it?
> I want something like the Input, where it shows different outputs according
> to the selected parameter from the select.
>
> Here is the XML code:
>
>
> 
> 
>
> 
>
> 
> FBK Format
> ShoweLab
> Format
> 
> 
> 
> 
> 
> 
> 
>
> 
> 
>  label="Training Dataset extracted from ${input_dataset.name}">
> format_condition["format_options"] ==
> "showelab"
>
> 
>  label="Validation Dataset extracted from ${input_dataset.name}">
> format_condition["format_options"] ==
> "showelab"
>
> 
>  label="Training Dataset extracted from ${input_dataset.name}">
> format_condition["format_options"]  == "fbk"
>
> 
> 
> format_condition["format_options"]  == "fbk"
>
> 
>  label="Validation Dataset extracted from ${input_dataset.name}">
> format_condition["format_options"]  == "fbk"
>
> 
> 
> format_condition["format_options"]  == "fbk"
> 
> 

You appear to have multiple defined datasets (three versions of
trainingDataset) which may be the problem, as the name is meant
to be unique.

I think you should have ONE  tag for trainingDataset but
set this up to switch output formats accordingly.

Peter
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Re: [galaxy-dev] Multiple output tools in Workflow

[Calogero Zarbo]

Hello Peter,

Thanks for your answer.

I tried your come but I am still not able to make it work the way I want.
I mean that in the workflow design page, when I switch the parameter, it
doesn't change the graphical list of outputs of the tool. How can I fix it?
I want something like the Input, where it shows different outputs according
to the selected parameter from the select.

Here is the XML code:







FBK Format
ShoweLab
Format










format_condition["format_options"] ==
"showelab"


format_condition["format_options"] ==
"showelab"


format_condition["format_options"]  == "fbk"


format_condition["format_options"]  == "fbk"


format_condition["format_options"]  == "fbk"


format_condition["format_options"]  == "fbk"







On Wed, Jul 16, 2014 at 6:54 PM, Peter Cock 
wrote:

> On Wed, Jul 16, 2014 at 5:28 PM, Calogero Zarbo  wrote:
> > Hello to everybody
> >
> > I'm developing my own tool that need to switch the numbers of output
> files
> > according to a parameter selected by the user from a list in the 
> > tag.
> > How can I do such thing?
> >
> > Here is the XML code:
> > 
> >  > format="showelab-dataset,fbk-svm-dataset"/>
> > 
> >
> > 
> > ".fbk-svm-dataset" Format
> >  selected="True">".showelab-dataset"
> > Format
> > 
> > 
> > 
> > 
> > 
> >
> > 
> > 
> >  > label="Training Dataset extracted from ${input_dataset.name}">
> > format_options == "showelab"
> > 
> >  > label="Validation Dataset extracted from ${input_dataset.name}">
> > format_options == "showelab"
> > 
> >  > label="Training Dataset extracted from ${input_dataset.name}">
> > format_options == "fbk"
> > 
> > 
> > format_options == "fbk"
> > 
> >  > label="Validation Dataset extracted from ${input_dataset.name}">
> > format_options == "fbk"
> > 
> >  label="Validation
> > Dataset Labels extracted from ${input_fbk_dataset_labels.name}">
> > format_options == "fbk"
> > 
> >
> > 
> >
> >
> > Basically I would like to have in the Workflow Canvas that the outputs
> > displayed in the interface will change according to the format_options
> > select parameter.
> >
> > Thanks in advance.
>
> Hi Calogero,
>
> I think this tool of mine would serve as a working example:
> https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id
>
> Peter
>



-- 
Calogero Zarbo


FBK - Fondazione Bruno Kessler
Center for Information Technology
Mpba - Predictive Models for Biomedicine & Environment
Via Sommarive, 18- 38123 Povo (Trento) IT
e-mail: za...@fbk.eu

phone: +39 0461 314 674
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Multiple output tools in Workflow

[Peter Cock]

On Wed, Jul 16, 2014 at 5:28 PM, Calogero Zarbo  wrote:
> Hello to everybody
>
> I'm developing my own tool that need to switch the numbers of output files
> according to a parameter selected by the user from a list in the 
> tag.
> How can I do such thing?
>
> Here is the XML code:
> 
>  format="showelab-dataset,fbk-svm-dataset"/>
> 
>
> 
> ".fbk-svm-dataset" Format
> ".showelab-dataset"
> Format
> 
> 
> 
> 
> 
>
> 
> 
>  label="Training Dataset extracted from ${input_dataset.name}">
> format_options == "showelab"
> 
>  label="Validation Dataset extracted from ${input_dataset.name}">
> format_options == "showelab"
> 
>  label="Training Dataset extracted from ${input_dataset.name}">
> format_options == "fbk"
> 
> 
> format_options == "fbk"
> 
>  label="Validation Dataset extracted from ${input_dataset.name}">
> format_options == "fbk"
> 
> 
> format_options == "fbk"
> 
>
> 
>
>
> Basically I would like to have in the Workflow Canvas that the outputs
> displayed in the interface will change according to the format_options
> select parameter.
>
> Thanks in advance.

Hi Calogero,

I think this tool of mine would serve as a working example:
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id

Peter
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[galaxy-dev] Multiple output tools in Workflow

[Calogero Zarbo]

Hello to everybody

I'm developing my own tool that need to switch the numbers of output files
according to a parameter selected by the user from a list in the 
tag.
How can I do such thing?

Here is the XML code:





".fbk-svm-dataset" Format
".showelab-dataset" Format









format_options == "showelab"


format_options == "showelab"


format_options == "fbk"


format_options == "fbk"


format_options == "fbk"


format_options == "fbk"





Basically I would like to have in the Workflow Canvas that the outputs
displayed in the interface will change according to the format_options
select parameter.

Thanks in advance.




-- 
Calogero Zarbo


FBK - Fondazione Bruno Kessler
Center for Information Technology
Mpba - Predictive Models for Biomedicine & Environment
Via Sommarive, 18- 38123 Povo (Trento) IT
e-mail: za...@fbk.eu

phone: +39 0461 314 674
___
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/