2015-06-30 11:04 GMT-05:00 John Chilton <jmchilton@gmail.com>:
On Mon, Jun 29, 2015 at 2:48 PM, Alexander Vowinkel <vowinkel.alexander@gmail.com> wrote:
I have a tool with filtered outputs (<data [..]><filter>[...]</data>).
A) As I understood the filters are pure python. But if I put it in "<![CDATA[", it doesn't work. I think this should work even better ;)
This sounds wrong - the standard library is handling the CDATA parsing for us and so Galaxy should be looking at an identical representation of the data. Are you sure you are using the CDATA tags correctly? I modified the test tool demonstrating output filters with the following patch (https://gist.github.com/jmchilton/1c8d13c01815a9b0fc8e) and ran the tool tests using the command:
./run_tests.sh -framework -id output_filter
and everything seemed fine.
Yeah. Weird. Now I don't have problems anymore too. Must have been something else.
B) The workflow generator doesn't interpret the filters. When I put the tool in a workflow, all possible outputs are shown. This doesn't change when I change an option that would change the output
choice.
Can someone fix this? ;)
This would be a nice enhancement - but it would take a lot of effort to implement. I would suspect we are going to be stuck with the display of invalid outputs for a while yet. I've created a Trello card for this issue:
What a pitty :(