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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