How can I populate a data_collection output ?

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How can I populate a data_collection output ?

juliech
Hi all,
I'm working with data_collection as type of input in xml files. but I
use all the datasets of a collection to compute some results that I
want to push in a "data_collection" output.
I know how take each dataset of a data_collection input with my
script, like this :
<configfile name="shscript">
...
for $f in $input
...
</configfile>
where $input is defined by <param name=$input1 type=data_collection
collection_type=list... in the top of my xml file.

But if my script produce some outputs (number of outputs not defined
in advance), how can I populate an output as a data_collection with my
shscript and how should I define this output in the xml ?

Thanks
Julie
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Re: How can I populate a data_collection output ?

John Chilton-4
Hello Julie,

  Right now Galaxy can implicitly create collections by running a tool
that takes in a single input or a paired dataset over say a list of
inputs or a list of paired inputs but tools cannot explicitly create
dataset collections. I think Galaxy's current capabilities add a lot
of useful functionality - but say tools that take a big input and
split it into an arbitrary number of pieces or tools that
normalize/summarize N inputs simultaneously and produce N outputs
cannot be represented. A few people made some progress on this at the
recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more
people have made it clear that it is an important feature.

Sorry.

-John


On Mon, Jul 28, 2014 at 11:47 AM, julie dubois <[hidden email]> wrote:

> Hi all,
> I'm working with data_collection as type of input in xml files. but I
> use all the datasets of a collection to compute some results that I
> want to push in a "data_collection" output.
> I know how take each dataset of a data_collection input with my
> script, like this :
> <configfile name="shscript">
> ...
> for $f in $input
> ...
> </configfile>
> where $input is defined by <param name=$input1 type=data_collection
> collection_type=list... in the top of my xml file.
>
> But if my script produce some outputs (number of outputs not defined
> in advance), how can I populate an output as a data_collection with my
> shscript and how should I define this output in the xml ?
>
> Thanks
> Julie
> ___________________________________________________________
> 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 can I populate a data_collection output ?

David Kelly
Hi John,

Is there any documentation that explains how dataset collections work? I'd like to learn more about it.

Thanks,
David


On Tue, Jul 29, 2014 at 3:20 PM, John Chilton <[hidden email]> wrote:
Hello Julie,

  Right now Galaxy can implicitly create collections by running a tool
that takes in a single input or a paired dataset over say a list of
inputs or a list of paired inputs but tools cannot explicitly create
dataset collections. I think Galaxy's current capabilities add a lot
of useful functionality - but say tools that take a big input and
split it into an arbitrary number of pieces or tools that
normalize/summarize N inputs simultaneously and produce N outputs
cannot be represented. A few people made some progress on this at the
recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more
people have made it clear that it is an important feature.

Sorry.

-John


On Mon, Jul 28, 2014 at 11:47 AM, julie dubois <[hidden email]> wrote:
> Hi all,
> I'm working with data_collection as type of input in xml files. but I
> use all the datasets of a collection to compute some results that I
> want to push in a "data_collection" output.
> I know how take each dataset of a data_collection input with my
> script, like this :
> <configfile name="shscript">
> ...
> for $f in $input
> ...
> </configfile>
> where $input is defined by <param name=$input1 type=data_collection
> collection_type=list... in the top of my xml file.
>
> But if my script produce some outputs (number of outputs not defined
> in advance), how can I populate an output as a data_collection with my
> shscript and how should I define this output in the xml ?
>
> Thanks
> Julie
> ___________________________________________________________
> 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
and other Galaxy lists, please use the interface at:
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Re: How can I populate a data_collection output ?

juliech
Hello John,
Thank you for your answer.
We shall thus wait.


Julie

2014-07-29 22:43 GMT+02:00 David Kelly <[hidden email]>:

> Hi John,
>
> Is there any documentation that explains how dataset collections work? I'd
> like to learn more about it.
>
> Thanks,
> David
>
>
> On Tue, Jul 29, 2014 at 3:20 PM, John Chilton <[hidden email]> wrote:
>>
>> Hello Julie,
>>
>>   Right now Galaxy can implicitly create collections by running a tool
>> that takes in a single input or a paired dataset over say a list of
>> inputs or a list of paired inputs but tools cannot explicitly create
>> dataset collections. I think Galaxy's current capabilities add a lot
>> of useful functionality - but say tools that take a big input and
>> split it into an arbitrary number of pieces or tools that
>> normalize/summarize N inputs simultaneously and produce N outputs
>> cannot be represented. A few people made some progress on this at the
>> recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more
>> people have made it clear that it is an important feature.
>>
>> Sorry.
>>
>> -John
>>
>>
>> On Mon, Jul 28, 2014 at 11:47 AM, julie dubois <[hidden email]> wrote:
>> > Hi all,
>> > I'm working with data_collection as type of input in xml files. but I
>> > use all the datasets of a collection to compute some results that I
>> > want to push in a "data_collection" output.
>> > I know how take each dataset of a data_collection input with my
>> > script, like this :
>> > <configfile name="shscript">
>> > ...
>> > for $f in $input
>> > ...
>> > </configfile>
>> > where $input is defined by <param name=$input1 type=data_collection
>> > collection_type=list... in the top of my xml file.
>> >
>> > But if my script produce some outputs (number of outputs not defined
>> > in advance), how can I populate an output as a data_collection with my
>> > shscript and how should I define this output in the xml ?
>> >
>> > Thanks
>> > Julie
>> > ___________________________________________________________
>> > 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:
>>   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 can I populate a data_collection output ?

John Chilton-4
In reply to this post by David Kelly
Hey David,

  Nothing on the wiki yet - the documentation I have been pointing
people at is my GCC 2014 presentation on this work
http://bit.ly/gcc2014workflows. It has details on tool developer side
of this as well as some end-user screenshots. There was some initial
support for dataset collections in the last (June) release - but they
will be more flushed out in the coming early August release and the
presentation describes features that were not in the June release but
will be in the August release.

  Hope this helps, feel free to ask me any questions as they come up.

-John



On Tue, Jul 29, 2014 at 4:43 PM, David Kelly <[hidden email]> wrote:

> Hi John,
>
> Is there any documentation that explains how dataset collections work? I'd
> like to learn more about it.
>
> Thanks,
> David
>
>
> On Tue, Jul 29, 2014 at 3:20 PM, John Chilton <[hidden email]> wrote:
>>
>> Hello Julie,
>>
>>   Right now Galaxy can implicitly create collections by running a tool
>> that takes in a single input or a paired dataset over say a list of
>> inputs or a list of paired inputs but tools cannot explicitly create
>> dataset collections. I think Galaxy's current capabilities add a lot
>> of useful functionality - but say tools that take a big input and
>> split it into an arbitrary number of pieces or tools that
>> normalize/summarize N inputs simultaneously and produce N outputs
>> cannot be represented. A few people made some progress on this at the
>> recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more
>> people have made it clear that it is an important feature.
>>
>> Sorry.
>>
>> -John
>>
>>
>> On Mon, Jul 28, 2014 at 11:47 AM, julie dubois <[hidden email]> wrote:
>> > Hi all,
>> > I'm working with data_collection as type of input in xml files. but I
>> > use all the datasets of a collection to compute some results that I
>> > want to push in a "data_collection" output.
>> > I know how take each dataset of a data_collection input with my
>> > script, like this :
>> > <configfile name="shscript">
>> > ...
>> > for $f in $input
>> > ...
>> > </configfile>
>> > where $input is defined by <param name=$input1 type=data_collection
>> > collection_type=list... in the top of my xml file.
>> >
>> > But if my script produce some outputs (number of outputs not defined
>> > in advance), how can I populate an output as a data_collection with my
>> > shscript and how should I define this output in the xml ?
>> >
>> > Thanks
>> > Julie
>> > ___________________________________________________________
>> > 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:
>>   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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To search Galaxy mailing lists use the unified search at:
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