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:
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