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:
<param name="bdg2" type="boolean" checked="False"
truevalue="-B2" falsevalue="" label="Save pileups in bedGraph?" />
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:
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,
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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