Hello John

Apologies for the delayed response, but many thanks for looking into this so thoroughly.


I've now tried running the test cases using planemo with the dev branch from github and all the cases pass that I expected to. (Using "bdg_options.bdg2" rather than "bdg_options|bdg2" to reference the parameter in the tests fails consistently, but I understand that this is normal behaviour so it's not a problem.)

So it looks to me like you've fixed this. I'm trying it now on my real tool tests where there are a few more moving parts but I don't see why it won't work there. I'll let you know if I do encounter any other strange cases.

Thanks again for taking the time to investigate and address these issues, it's greatly appreciated.

Best wishes

Peter

On 20/05/15 20:55, John Chilton wrote:
Peter - thanks for the detailed bug report!

I believe this should be fixed with the following PR
(https://github.com/galaxyproject/galaxy/pull/273) that has been
merged into release_15.05 on github as well as the dev branch. I tried
to fixed a few different bugs related to boolean and select handling
with in the confines of tests - so let me know if it didn't fix this
exact use case and I will look at it some more.

There is now this test case that verifies the correctness of boolean
test parameters inside of conditionals
(https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/boolean_conditional.xml)
- let me know if you see anything wrong with it. The test can be run
with by executing:

./run_tests.sh -framework -id boolean_conditional

from Galaxy's root.

Thanks again,
-John

On Tue, May 19, 2015 at 10:01 AM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
Hello

I've encountered a problem with my tool tests when using a boolean as the
"control" parameter within a conditional: it doesn't appear to be possible
to change the value from the default "true" or "false" values within the
tests.

For example if I have a boolean 'bdg2' which controls a conditional block
and which defaults to its falsevalue:

   ...
   <conditional name="bdg_options">
     <param name="bdg2" type="boolean" checked="False"
            truevalue="-B2" falsevalue="" label="Save pileups in bedGraph?"
/>
     <when value="-B2">
   ...

and then try to set the value within a test using:

     <param name="bdg_options|bdg2" value="true" />

then the value remains unchanged from the default when the tests are run.
(Similarly if I set checked="True" then the value in the tests is always
"True" regardless of the value I try to set.)

I've tried various ways of referencing the parameter (e.g.
'bdg_options|bdg2', 'bdg2' and 'bdg_options') but none of these work for me.

Am I doing something obviously wrong? (nb this is a different problem from
my previous post about setting boolean values in tests - that works fine for
booleans which are not conditional control parameters).

I've made a small example tool to investigate the issue, the files are here:

https://gist.github.com/pjbriggs/c27e4366dfcdd6d96cb2

and using planemo 0.11.1 to run the tests.

(On a side note, it also seems that within the <command> section, the values
returned for this type of boolean only ever appear to be 'True' or 'False' -
but it seems okay to match against the truevalue and falsevalues in the
<when> tag.)

Thanks for any help,

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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