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:


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