Hi.
I'm still searching for a solution to this problem.
Currently we have to implement a tool to read the GTF file selected
via a from_data_table parameter and output a list of feature types.
Secondly we have a second tool that reads this file using a
from_dataset parameter so the user ca
Hi Greg,
thanks for the suggestion. This line doesn't seem to work:
Galaxy looks for a file at galaxy_dir/tool-data/some_value rather than
the value given in the .loc file
I would also like to be able to use the galaxy data tables rather then
referring directly to a .loc file.
Any ide
Hi Shaun,
This should be possible. It's been quite a long time since I worked on tools,
so maybe others can provide better assistance if I am incorrect here. You'll
need to have a conditional something like the following ( not tested whatsoever
):
Hi Greg, I'm not sure if this answers my question. Using
options_from_file is fine if I want to refer to the same file each time.
In this case I want the first select to choose which gtf file to look
at (by species) and the second select to pull options (gtf annotation
types) from this fi
Hello Shaun,
Use the 'from_file' option. The referenced file should be in the ~/tool-data
directory in the Galaxy root. There are several example tools in the
distribution that use this option. Here is the example code from the
annotation profiler tool:
and here is an example from the mic
