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(a)gmail.com> wrote:
Hi,
I'm working on the project for Google Summer of Code:
https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Co...
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