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. Thanks, Jon -----Original Message----- From: Bossers, Alex [mailto:Alex.Bossers@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? 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-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Jon Sorenson [JSorenson@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