[galaxy-user] Aggregate collections of files (example: Heatmaps)

[Ted Goldstein]

I  am developing several tools that will need to read and write multiple data 
files at once. For example, Eisen Cluster produces a  heatmap which consists of 
three files: a .cdt file,  .atr file and a gtr file which are the underlying 
heatmap and the array tree and the gene tree.  All three files need to be kept 
together.  I guess I could wrap them in a zip file and pack and unpack them.
The heatmap is not just a view only object. Some tools, such as cuttree, would 
extract one tree and then aggregate genes (or arrays)  below a certain depth 
and create a new trio of files.  Is there support  for (or plans for creating) 
any aggregate data types?

Thanks
Ted

CBSE, UCSC
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] Aggregate collections of files (example: Heatmaps)

[Peter Cock]

On Tue, Aug 21, 2012 at 4:46 PM, Ted Goldstein t...@soe.ucsc.edu wrote:
 I  am developing several tools that will need to read and write multiple
 data files at once. For example, Eisen Cluster produces a  heatmap
 which consists of three files: a .cdt file,  .atr file and a gtr file which 
 are
 the underlying heatmap and the array tree and the gene tree.  All three
 files need to be kept together.  I guess I could wrap them in a zip file
 and pack and unpack them.The heatmap is not just a view only
 object. Some tools, such as cuttree, would extract one tree and then
 aggregate genes (or arrays)  below a certain depth and create a new
 trio of files.  Is there support  for (or plans for creating) any aggregate
 data types?

Hi Ted,

There is support for composite datatypes, so this should be possible.
http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes

This kind of discussion is normally directed to the galaxy-dev list (CC'd)

Peter
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/