Hi Peter, thanks a lot for your quick reply. However "&>" doesn't seem to work as well. Also, I do have to admit that two different "doesn't work" exist. Notations that are not accepted during parsing of toolxy.xml: &> \&> \\&> Notations that are accepted, but don't produce any content written to "$logFile": &> &> &> Any other suggestions? Cheers, Uwe -----Ursprüngliche Nachricht----- Von: Peter Cock [mailto:p.j.a.cock@googlemail.com] Gesendet: Montag, 24. Oktober 2011 10:06 An: Appelt, Uwe Cc: galaxy-user@lists.bx.psu.edu Betreff: Re: [galaxy-user] tool.xml "&>" console redirection within command-tag On Mon, Oct 24, 2011 at 9:01 AM, Appelt, Uwe <uwe.appelt@nct-heidelberg.de> wrote:
Dear all,
that has probably been asked 10e6 times, however, I don't find any comments on how to properly escape special characters in a toolxy.xml. What I want to achieve is the following:
<command interpreter="bash">$myScript &> $logFile</command>
where myScript is dynamically created (as part of the configfiles-section) and the logFile is where stderr and stdout should go to. Now the problem is obviously the "&"-character, because it causes the following error-msg on reloading the toolxy.xml:
ExpatError: not well-formed (invalid token): line 5, column 50
where the 5/50 refers to the "&"-character. By the way: redirecting either stdout or stderr by specifying just ">" (instead of "&>") works fine.
I tried a lot of different notations in the meanwhile, but neither something like "\&>" nor "\&>" works. Any suggestions?
Many thanks in advance and Cheers! Uwe
Don't you need to escape both the & and the > characters here? i.e. &> should work. Peter