Jon,
you might want to have a look at the ALLOWED CHARACTERS section of the tool xml 
configuration pages on the wiki. Need to add these to your config.
Seems like the ; gets masked to X.
Alex


________________________________
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
namens Jon Sorenson [jsoren...@pacificbiosciences.com]
Verzonden: zaterdag 28 mei 2011 7:01
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] semi-colons converted to X in config file?

I suspect I’ve run into a rare XML entity/Cheetah conversion bug.

I have a parameter definition like
<param name="schedule" type="text" 
value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" 
label="Parameter Schedule" size="60"/>

I also am creating a configfile using
<configfile name="iniFile">
…
paramSchedule=${schedule}
…
</configfile>

The file that gets created has
…
paramSchedule=6,3,75X6,3,75X5,3,75X5,3,75X6,2,75X6,2,75X5,2,75X5,2,75
…

i.e. the ‘;’ character gets converted to X.  I suspect that this is an XML 
parsing issue (trying to interpret ‘;’ as marking an entity resolution?) but 
the default value get displayed correctly in the Galaxy UI so it might not be 
so simple as this.  I can’t see how Cheetah is converting ‘;’ to ‘X’ but maybe 
that’s it.

I’m planning on hacking around this, but wanted to post to the list to see if 
anyone else has seen this or has quick recommendations.

Jon


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