Dataset_Collections : an example of code for a tool ?
Hi, Your latest update is very exciting with the introduction of Dataset_Collections!!! It's very useful for us . I've been testing it in a new install of Galaxy and I can create a Dataset_Collection in my history. But with the reading of trello cards and this presentation : https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhufI... I've not yet found how to code a tool to use this collection and/or unique dataset. Is it possible to have the bowtie2 version (and or Merge Bam) with these 2 possibilities to have an example? And how can I see the icons in the formular which allow to switch between the use of unique dataset and the use of dataset collection, like is presented in the presentation ? Thanks. Julie
Hello Julie, Thanks for your interest in dataset collections! Good luck with your experiments and sorry about the bumps in road you will experience - these are early days :). Here are the modified tools from the example: https://gist.github.com/jmchilton/b6773c8433224ea7ed78 These examples may not make sense because the example in the presentation is highly contrived. There are some equally contrived - but much simpler tools (to visualize, test the concepts) - in Galaxy's test tools directory (https://bitbucket.org/galaxy/galaxy-central/src/default/test/functional/tool...) see collection_mixed_param.xml, collection_nested_test.xml, and collection_paired_test.xml. Hope this helps. -John On Wed, Jun 4, 2014 at 9:40 AM, julie dubois <dubjulie@gmail.com> wrote:
Hi, Your latest update is very exciting with the introduction of Dataset_Collections!!! It's very useful for us . I've been testing it in a new install of Galaxy and I can create a Dataset_Collection in my history. But with the reading of trello cards and this presentation : https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhufI... I've not yet found how to code a tool to use this collection and/or unique dataset.
Is it possible to have the bowtie2 version (and or Merge Bam) with these 2 possibilities to have an example? And how can I see the icons in the formular which allow to switch between the use of unique dataset and the use of dataset collection, like is presented in the presentation ?
Thanks.
Julie
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Thanks a lot !!! I think other questions will appear with the use of collections in workflows, but it will be an other story :) Julie 2014-06-04 17:00 GMT+02:00 John Chilton <jmchilton@gmail.com>:
Hello Julie,
Thanks for your interest in dataset collections! Good luck with your experiments and sorry about the bumps in road you will experience - these are early days :). Here are the modified tools from the example:
https://gist.github.com/jmchilton/b6773c8433224ea7ed78
These examples may not make sense because the example in the presentation is highly contrived. There are some equally contrived - but much simpler tools (to visualize, test the concepts) - in Galaxy's test tools directory ( https://bitbucket.org/galaxy/galaxy-central/src/default/test/functional/tool... ) see collection_mixed_param.xml, collection_nested_test.xml, and collection_paired_test.xml.
Hope this helps.
-John
On Wed, Jun 4, 2014 at 9:40 AM, julie dubois <dubjulie@gmail.com> wrote:
Hi, Your latest update is very exciting with the introduction of Dataset_Collections!!! It's very useful for us . I've been testing it in a new install of Galaxy and I can create a Dataset_Collection in my history. But with the reading of trello cards and this presentation :
https://docs.google.com/presentation/d/1D4pbULfe3IbSRVF3xsWvp9GyAct4SNfHhufI...
I've not yet found how to code a tool to use this collection and/or unique dataset.
Is it possible to have the bowtie2 version (and or Merge Bam) with these 2 possibilities to have an example? And how can I see the icons in the formular which allow to switch between the use of unique dataset and the use of dataset collection, like is presented in the presentation ?
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/
participants (2)
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John Chilton -
julie dubois