Hi,

update: My composite datatype is now created properly. When I upload my "component" file in "Upload file" tool with "file format" set to point my datatype everything is OK - generate_primary_file method is called and "primary" file is generated. However, I'm unable to achieve this when "component" files are created by my tool.

Thanks, Filip Balejko

On Fri, Jun 18, 2010 at 18:09, Filip Balejko filip.balejko@gmail.com wrote:

Hi,

I'm working on the project for Google Summer of Code: https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_...

It was going smooth but today I've got stuck and I would really appreciate your help.

I'm trying to create a Composite Datatype according to:

http://bitbucket.org/galaxy/galaxy-central/wiki/CompositeDatatypes

Currently I'm passing $output.files_path to my .py script and then I'm creating my "component" files in this directory. As I've understood from documentation, generate_primary_file method is where I should generate my "primary" output. But It seems that my composite datatype object isn't created - I'm logging some debug in __init__ and generate_primary_file but nothing shows up. Of course I've added this datatype to datatypes_conf.xml.

Have I misunderstood something? Should I do something else to get it working?

I've looked into:

lib/galaxy/datatypes/genetics.py tools/rgenetics/rgfakePed.xml tools/rgenetics/rgfakePed.py

and it seems to me that this tool creates its "primary" output in rgfakePed.py (doImport function) and I can't figure out when generate_primary_file method (genetics.py:  Rgenetics()) is being called.

Thanks, Filip Balejko