Thanks!  This has been fixed in changeset 5594:2f84c42a548a.

Also, if I could ask for a minor thing to assist us with list
maintenance: when starting a new thread on the list, please create a
brand new email to galaxy-dev rather than replying to an existing
message.  Replying includes headers that reference the message you
replied to, which means it threads with the original thread in mail
readers and the list archive.

Thanks,
--nate

Louise-Amélie Schmitt wrote:
> Yeah, and I fixed it... somehow.
> 
> In the lib/galaxy/web/form_builder.py I added the import on
> string_as_bool from galaxy.util, then I modified the code as
> follows:
> 
> 126     @staticmethod
> 127     def is_checked( value ):
> 128         if value == True:
> 129             return True
> 130         # This may look strange upon initial inspection, but see
> the comments in the get_html() method
> 131         # above for clarification.  Basically, if value is not
> True, then it will always be a list with
> 132         # 2 input fields ( a checkbox and a hidden field ) if
> the checkbox is checked.  If it is not
> 133         # checked, then value will be only the hidden field.
> 134         if isinstance(value, basestring):
> 135             return string_as_bool( value )
> 136         return isinstance( value, list ) and len( value ) == 2
> 
> (see l.134 and 135)
> The value variable actually contained something else than True or a
> list, namely the string "true".
> Now it seems to work fine.
> 
> Cheers,
> L-A
> 
> 
> Le 23/05/2011 18:26, Peter Cock a écrit :
> >2011/5/23 Louise-Amélie Schmitt<louise-amelie.schm...@embl.de>:
> >>@ Peter: I'm not sure I can get more precise... the checked attribute has no
> >>effect whatsoever, the boxes are always unchecked when I open the tool. I
> >>tried the "yes" and the "true" values to no avail.
> >>
> >>@ Leandro: Yes I already saw that ...
> >>
> >>But that's actually not the issue here. I just want my checkboxes to be
> >>checked by default, and it appears not to work.
> >>
> >>To give an example, here is one of the lines of my tool XML file:
> >><param name="SQA" type="boolean" label="Run SolexaQA" checked="true" />
> >>This checkbox remains unchecked at tool opening.
> >>
> >>As far as I know, some people managed to get it working and I'd like to know
> >>how.
> >>
> >>Any suggestion?
> >I think you've found a bug :(
> >
> >I found two working examples, "Filter out low complexity regions (with
> >DUST)" parameter in tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml and
> >the scaffolding parameter in sr_assembly/velvetg.xml - however they
> >are both within a conditional parameter section (only shown in
> >advanced mode).
> >
> >Have a look at sr_mapping/bwa_color_wrapper.xml which has a "Suppress
> >the header in the output SAM file" boolean which should be checked by
> >default:
> >
> ><param name="suppressHeader" type="boolean" truevalue="true"
> >falsevalue="false" checked="true" label="Suppress the header in the
> >output SAM file" help="BWA produces SAM with several lines of header
> >information" />
> >
> >It's not working on http://usegalaxy.org - the box isn't checked.
> >
> >If you can verify that, please file an issue on bitbucket:
> >https://bitbucket.org/galaxy/galaxy-central/issues/new
> >
> >Peter
> 
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