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