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
in the configfile (and it works for this limited purpose) but adding a custom
sanitizer seems like the appropriate and robust thing to do.
From: Bossers, Alex [mailto:alex.boss...@wur.nl]
Sent: Saturday, May 28, 2011 10:34 AM
To: Jon Sorenson; firstname.lastname@example.org
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
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
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
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.
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: