How to build an application that uses a set of files?

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How to build an application that uses a set of files?

georgeweingart

Hello,


I would like to get advice how to implement the following application into Galaxy:


We have a set of say, 17 tabular files,   we would like to present them to the User and allow him to select a subset of them,  say 9.

Once he selected these files we would like to invoke our program “merge.py”  against the subset of 9 files the User selected whose result is an output of one file.

How would the xml look?


Thanks!
George Weingart



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Re: How to build an application that uses a set of files?

John Chilton-4
Are these 17 files fairly dynamic - i.e. are they going to depend on
previous steps in a history or user uploads - or are they literally
just 17 more or less fixed files associated with that tool and every
user should see roughly the same 17 options.

-John

On Thu, Aug 21, 2014 at 3:03 PM, George Weingart
<[hidden email]> wrote:

> Hello,
>
>
> I would like to get advice how to implement the following application into
> Galaxy:
>
>
> We have a set of say, 17 tabular files,   we would like to present them to
> the User and allow him to select a subset of them,  say 9.
>
> Once he selected these files we would like to invoke our program “merge.py”
> against the subset of 9 files the User selected whose result is an output of
> one file.
>
> How would the xml look?
>
>
> Thanks!
> George Weingart
>
>
>
> ___________________________________________________________
> 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/

___________________________________________________________
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Re: How to build an application that uses a set of files?

georgeweingart
They are totally dynamic.
Say all the files of tabular type that the User has at the moment.


On Thu, Aug 21, 2014 at 12:28 PM, John Chilton <[hidden email]> wrote:
Are these 17 files fairly dynamic - i.e. are they going to depend on
previous steps in a history or user uploads - or are they literally
just 17 more or less fixed files associated with that tool and every
user should see roughly the same 17 options.

-John

On Thu, Aug 21, 2014 at 3:03 PM, George Weingart
<[hidden email]> wrote:
> Hello,
>
>
> I would like to get advice how to implement the following application into
> Galaxy:
>
>
> We have a set of say, 17 tabular files,   we would like to present them to
> the User and allow him to select a subset of them,  say 9.
>
> Once he selected these files we would like to invoke our program “merge.py”
> against the subset of 9 files the User selected whose result is an output of
> one file.
>
> How would the xml look?
>
>
> Thanks!
> George Weingart
>
>
>
> ___________________________________________________________
> 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/


___________________________________________________________
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Re: How to build an application that uses a set of files?

John Chilton-4
Hmm... in that case I think you can just create a multiple input data parameter.

<input type="data" format="tabular" multiple="true" name="inputs"
label="blah" />

You can iterate through the files in your <command> tag and pass them
to your merge.py file:

<command interpreter="python">merge.py #for $input in $inputs# $input
#end for# ...
</command>

This works unless you literally need 9 files - this input type doesn't
support min/max right now. (There is a Trello card that includes
adding such functionality if you want to vote on it
https://trello.com/c/lp5YmA1O).

I hope this helps - let me know if this is not quite right.

-John


On Thu, Aug 21, 2014 at 3:30 PM, George Weingart
<[hidden email]> wrote:

> They are totally dynamic.
> Say all the files of tabular type that the User has at the moment.
>
>
> On Thu, Aug 21, 2014 at 12:28 PM, John Chilton <[hidden email]> wrote:
>>
>> Are these 17 files fairly dynamic - i.e. are they going to depend on
>> previous steps in a history or user uploads - or are they literally
>> just 17 more or less fixed files associated with that tool and every
>> user should see roughly the same 17 options.
>>
>> -John
>>
>> On Thu, Aug 21, 2014 at 3:03 PM, George Weingart
>> <[hidden email]> wrote:
>> > Hello,
>> >
>> >
>> > I would like to get advice how to implement the following application
>> > into
>> > Galaxy:
>> >
>> >
>> > We have a set of say, 17 tabular files,   we would like to present them
>> > to
>> > the User and allow him to select a subset of them,  say 9.
>> >
>> > Once he selected these files we would like to invoke our program
>> > “merge.py”
>> > against the subset of 9 files the User selected whose result is an
>> > output of
>> > one file.
>> >
>> > How would the xml look?
>> >
>> >
>> > Thanks!
>> > George Weingart
>> >
>> >
>> >
>> > ___________________________________________________________
>> > 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/
>
>

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in your mail client.  To manage your subscriptions to this
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Re: How to build an application that uses a set of files?

georgeweingart
Hi John,
Worked on first try!
Thanks!!!!!
George Weingart PhD



On Thu, Aug 21, 2014 at 12:43 PM, John Chilton <[hidden email]> wrote:
Hmm... in that case I think you can just create a multiple input data parameter.

<input type="data" format="tabular" multiple="true" name="inputs"
label="blah" />

You can iterate through the files in your <command> tag and pass them
to your merge.py file:

<command interpreter="python">merge.py #for $input in $inputs# $input
#end for# ...
</command>

This works unless you literally need 9 files - this input type doesn't
support min/max right now. (There is a Trello card that includes
adding such functionality if you want to vote on it
https://trello.com/c/lp5YmA1O).

I hope this helps - let me know if this is not quite right.

-John


On Thu, Aug 21, 2014 at 3:30 PM, George Weingart
<[hidden email]> wrote:
> They are totally dynamic.
> Say all the files of tabular type that the User has at the moment.
>
>
> On Thu, Aug 21, 2014 at 12:28 PM, John Chilton <[hidden email]> wrote:
>>
>> Are these 17 files fairly dynamic - i.e. are they going to depend on
>> previous steps in a history or user uploads - or are they literally
>> just 17 more or less fixed files associated with that tool and every
>> user should see roughly the same 17 options.
>>
>> -John
>>
>> On Thu, Aug 21, 2014 at 3:03 PM, George Weingart
>> <[hidden email]> wrote:
>> > Hello,
>> >
>> >
>> > I would like to get advice how to implement the following application
>> > into
>> > Galaxy:
>> >
>> >
>> > We have a set of say, 17 tabular files,   we would like to present them
>> > to
>> > the User and allow him to select a subset of them,  say 9.
>> >
>> > Once he selected these files we would like to invoke our program
>> > “merge.py”
>> > against the subset of 9 files the User selected whose result is an
>> > output of
>> > one file.
>> >
>> > How would the xml look?
>> >
>> >
>> > Thanks!
>> > George Weingart
>> >
>> >
>> >
>> > ___________________________________________________________
>> > 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/
>
>


___________________________________________________________
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:
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