Hi John,

Are you saying that "composite multiple file dataset" isn't required and won't 
be implemented?

We are using your implementation of multifiles dataset ("m:xxx" type) and hope 
that eventually it will be pushed into main Galaxy implementation.

As we are using Galaxy for CT reconstruction tools, where input and output can 
consist of a couple thousand files, other options are not feasible, i.e. 
grouping datasets.

-Alex

-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John Chilton
Sent: Thursday, 28 February 2013 2:06 AM
To: Jeremy Goecks
Cc: Jim Johnson; <galaxy-...@bx.psu.edu>
Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff

Hey Jeremy,

  I am trying to think about a path forward with this composite multiple file 
dataset implementation. It seems there is consensus among the galaxy team that 
it shouldn't be included because grouping actual datasets would be superior. In 
that light, I am revisiting this e-mail, because depending on the 
implementation of what you described multiple file datasets are a specific case 
of this concept with some likely uncontroversial enhancements for the specific 
case of composite datatypes that are a homogeneous list of files. Does that 
make any sense?

  If I implemented (i) and (ii) in such a way that the multiple file dataset 
stuff flowed out more organically is there any chance than it could be included 
in galaxy-central. If no and the implicit datatypes and parallelism stuff would 
remain no-gos implementing what you described would still benefit the multiple 
file datasets implementation, so I still might do this, would a clean 
implementation of just what you described be accepted?

  Any thoughts you or anyone has on the future direction of composite datatypes 
in general would be appreciated?

Thanks for your time,
-John


On Fri, Oct 12, 2012 at 2:44 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
> Hi Jim,
>
> This is nice and is a path forward for the immediate future.
>
> That said, a couple extensions to Galaxy to better support composite 
> datatypes would enable cummerbund without the additional tools:
>
> (i) extending the composite datatype to include definition of 
> individual outputs in the collection;
> (ii) extend the history panel to allow usage/selection of (1) the 
> complete composite set of files or (2) individual items in a composite 
> datatype
>
> Once (i) is done, (ii) should be straightforward using the new history 
> panel code.
>
> Of course, the advantage of these extensions is that they'd address 
> both cummerbund issues as well as other challenges, such as using 
> output from the barcode splitter.
>
> J.
>
> On Oct 11, 2012, at 6:14 PM, Jim Johnson wrote:
>
> Checking to see if there is any interest in including a parameter 
> option to select outputs for cuffdiff, potentially including a 
> composite output and a cummeRbund sqlite database.
>
> Issues:
>   cuffdiff produces 21 output files, which is a little unwieldy in a 
> galaxy history.
>   cummeRbund generates its database when given a cuffdiff output 
> directory, but manually hooking up 21 outputs to the cummerbund_wrapper is a 
> pain.
>
> I've put demo code in the testtoolshed under the name repository name 
> cummerbund
>     
> http://jjohn...@testtoolshed.g2.bx.psu.edu/repos/jjohnson/cummerbund
>
> This includes new datatypes defined in datatypes_conf.xml and 
> implemented in
> cuffdata.py:
>       <!-- html composite dataset with cuffdiff outputs in the extra 
> files path -->
>       <datatype extension="cuffdata"
> type="galaxy.datatypes.cuffdata:CuffDiffData"/>
>       <!-- cummeRbund SQLite database -->
>       <datatype extension="cuffdatadb"
> type="galaxy.datatypes.cuffdata:CuffDataDB"/>
>
> The cuffdiff wrapper has a multiple select parameter to choose which 
> output files to put in the history.
> In addition to the 21 cuffdiff outputs, the wrapper can also generate:
>   cuffdata - which is a composite HTML output with links to the 21 
> cuffdiff outputs
>   cuffdatadb - which is the cummeRbund SQLite database
>
> I also added utility tools:
>   cuffdata_datasets - which will take files from the composite 
> cuffdata and copy them as datasets into the history
>   cuffdata_cummerbund - which generates the cummeRbund cuffdatadb from 
> the composite cuffdata
>
> I updated the cummerbund_wrapper:
>   with tryCatch so that a R error on a plot won't exit the Rscript
>   to include a small image of each plot on the html page
>   added plots for : dispersion, scatter matrix, MDS, and PCA
>
> Thanks,
> JJ
>
>
>
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