Conditional tool options based on input file format?

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Conditional tool options based on input file format?

Peter Cock
Dear all,

I've looked over the wiki and as far as I can see, 'when' tags used inside
'conditional' tags only work on another input variable's values.

I would like to be able to do is a conditional based on the file format
of an input file. For instance, a tool might take XML or tabular files,
and need to show additional parameters for one input type but not the
other.

Does this enhancement idea seem useful?

Peter
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Re: Conditional tool options based on input file format?

Peter Cock
On Wed, Apr 18, 2012 at 12:01 PM, Peter Cock <[hidden email]> wrote:

> Dear all,
>
> I've looked over the wiki and as far as I can see, 'when' tags used inside
> 'conditional' tags only work on another input variable's values.
>
> I would like to be able to do is a conditional based on the file format
> of an input file. For instance, a tool might take XML or tabular files,
> and need to show additional parameters for one input type but not the
> other.
>
> Does this enhancement idea seem useful?
>
> Peter

Hello again,

I'd still like to be able to show different tool parameters for different
input file formats - is anyone else interested in using or working on
this?

Thanks,

Peter
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Re: Conditional tool options based on input file format?

Björn Grüning
Hi Peter,

> > I've looked over the wiki and as far as I can see, 'when' tags used inside
> > 'conditional' tags only work on another input variable's values.
> >
> > I would like to be able to do is a conditional based on the file format
> > of an input file. For instance, a tool might take XML or tabular files,
> > and need to show additional parameters for one input type but not the
> > other.
> >
> > Does this enhancement idea seem useful?
> >
> > Peter
>
> Hello again,
>
> I'd still like to be able to show different tool parameters for different
> input file formats - is anyone else interested in using or working on
> this?

Yes! Im using that for a few of my tools, but currently the user need to
choose the file format, that is suboptimal :(
But i have no time for a proper solution, a few of your reviews are also
waiting ... :(

Sorry,
Bjoern

> Thanks,
>
> Peter
> ___________________________________________________________
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Re: Conditional tool options based on input file format?

John Chilton
In reply to this post by Peter Cock
Hey Peter,

I wonder if it is better to ask the user what type they would like to
select and then have the input param inside the conditional. My
concern about you approach is who it would interplay with workflows.
Say you build a workflow that processes XML files with one input, say
an XML file. If that input param had let you select multiple formats
(format="tabular,xml"), then I believe the workflow input will as well
even though the options as well, even though the workflow would not be
valid for the other types.

-John


On Fri, Mar 15, 2013 at 9:43 AM, Peter Cock <[hidden email]> wrote:

> On Wed, Apr 18, 2012 at 12:01 PM, Peter Cock <[hidden email]> wrote:
>> Dear all,
>>
>> I've looked over the wiki and as far as I can see, 'when' tags used inside
>> 'conditional' tags only work on another input variable's values.
>>
>> I would like to be able to do is a conditional based on the file format
>> of an input file. For instance, a tool might take XML or tabular files,
>> and need to show additional parameters for one input type but not the
>> other.
>>
>> Does this enhancement idea seem useful?
>>
>> Peter
>
> Hello again,
>
> I'd still like to be able to show different tool parameters for different
> input file formats - is anyone else interested in using or working on
> this?
>
> Thanks,
>
> Peter
> ___________________________________________________________
> 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/
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Re: Conditional tool options based on input file format?

Peter Cock
On Fri, Mar 15, 2013 at 2:51 PM, John Chilton <[hidden email]> wrote:
> Hey Peter,
>
> I wonder if it is better to ask the user what type they would like to
> select and then have the input param inside the conditional.

That is doable now, but I'm not sure it is optimal for usability.

> My
> concern about you approach is who it would interplay with workflows.
> Say you build a workflow that processes XML files with one input, say
> an XML file. If that input param had let you select multiple formats
> (format="tabular,xml"), then I believe the workflow input will as well
> even though the options as well, even though the workflow would not be
> valid for the other types.
>
> -John

Good point... I'm not sure what the workflow would currently allow
here - just XML, or both tabular and XML.

I guess a side effect of my format specific options would be that a
workflow using such a tool should be locked to just the one format.
Is that such a bad thing?

Peter
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Re: Conditional tool options based on input file format?

John Chilton-2
On Fri, Mar 15, 2013 at 9:58 AM, Peter Cock <[hidden email]> wrote:

> On Fri, Mar 15, 2013 at 2:51 PM, John Chilton <[hidden email]> wrote:
>> Hey Peter,
>>
>> I wonder if it is better to ask the user what type they would like to
>> select and then have the input param inside the conditional.
>
> That is doable now, but I'm not sure it is optimal for usability.
>
>> My
>> concern about you approach is who it would interplay with workflows.
>> Say you build a workflow that processes XML files with one input, say
>> an XML file. If that input param had let you select multiple formats
>> (format="tabular,xml"), then I believe the workflow input will as well
>> even though the options as well, even though the workflow would not be
>> valid for the other types.
>>
>> -John
>
> Good point... I'm not sure what the workflow would currently allow
> here - just XML, or both tabular and XML.
>
> I guess a side effect of my format specific options would be that a
> workflow using such a tool should be locked to just the one format.

Excellent point, I tend to be a pessimist about this sort of thing but
you are indeed right and that would be a good solution.

-John

> Is that such a bad thing?
>
> Peter
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Re: Conditional tool options based on input file format?

Peter Cock
In reply to this post by Björn Grüning
On Fri, Mar 15, 2013 at 2:50 PM, Björn Grüning
<[hidden email]> wrote:

> Hi Peter,
>
>> > I've looked over the wiki and as far as I can see, 'when' tags used inside
>> > 'conditional' tags only work on another input variable's values.
>> >
>> > I would like to be able to do is a conditional based on the file format
>> > of an input file. For instance, a tool might take XML or tabular files,
>> > and need to show additional parameters for one input type but not the
>> > other.
>> >
>> > Does this enhancement idea seem useful?
>> >
>> > Peter
>>
>> Hello again,
>>
>> I'd still like to be able to show different tool parameters for different
>> input file formats - is anyone else interested in using or working on
>> this?
>
> Yes! Im using that for a few of my tools, but currently the user need to
> choose the file format, that is suboptimal :(

Thank Bjoern & John for your comments back in March.
I've just filed a Trello card for this:
https://trello.com/card/-/506338ce32ae458f6d15e4b3/837

This was prompted by revisiting my Venn Diagram tool, where it
would be nice to offer a column number parameter when using
a tabular input file (but this is not appropriate for FASTA files):
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list

Peter

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