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
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 dubjulie@gmail.com 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/
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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 jmchilton@gmail.com 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 dubjulie@gmail.com 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/
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Hello John, Thank you for your answer. We shall thus wait.
Julie
2014-07-29 22:43 GMT+02:00 David Kelly davidkelly@uchicago.edu:
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 jmchilton@gmail.com 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 dubjulie@gmail.com 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/
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 davidkelly@uchicago.edu 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 jmchilton@gmail.com 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 dubjulie@gmail.com 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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