On Mon, Mar 25, 2013 at 2:16 PM, Alexandre Loywick a.loywick@gmail.com wrote:

Hi galaxians,

I'm having an issue with tool parameters when using conditional tag and boolean parameters.

My xml is like this:

<conditional name="mis_allowed_conditional"> <param name="mis_allowed_bool" type="boolean" label="Allow mismatch ?" truevalue="-m" falsevalue="" checked="no"/> <when value="-m"> <param name="mis_allowed" type="float" value="0"/> </when> </conditional>

and my command line is like:

<command interpreter="python">wrapper.py $mis_allowed_conditional.mis_allowed_bool $mis_allowed_conditional.mis_allowed</command>

The problem is when mis_allowed_bool isn't checked, I don't have any arguments in my command line (as expected). But, when it is checked, $mis_allowed_conditional.mis_allowed_bool is set to "True" and not to "-m". The strange thing is that the "mis_allowed" textfield is visible when mis_allowed_bool is checked so I guess that the when behaves as expected. Moreover, other boolean parameters that are not nested in a conditional work as they should.

Is there something wrong with my xml or is this some kind of bug?

It sounds similar to a an old bug which was fixed in June 2011, BitBucket Issue 393: Can't use checkbox (boolean) with conditional parameters https://bitbucket.org/galaxy/galaxy-central/issue/393/ [DEAD LINK]

I can't find the matching entry on Trello though... so maybe only open issues were migrated?

The workaround was to use a select with two options.

Peter