Ah, that's it.  Thanks.  I had skimmed over the section on the optional 
sanitizer part of param definitions and didn't realize there was some default 
sanitization occurring.  Without understanding this problem, I had hacked 
around it with
#set $schedule2=$schedule.replace('X',';')
in the configfile (and it works for this limited purpose) but adding a custom 
sanitizer seems like the appropriate and robust thing to do.



-----Original Message-----
From: Bossers, Alex [mailto:alex.boss...@wur.nl] 
Sent: Saturday, May 28, 2011 10:34 AM
To: Jon Sorenson; galaxy-dev@lists.bx.psu.edu
Subject: RE: semi-colons converted to X in config file?

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.

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" 
label="Parameter Schedule" size="60"/>

I also am creating a configfile using
<configfile name="iniFile">

The file that gets created has

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.


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