On Mon, Dec 12, 2011 at 4:34 PM, <domantas.motiejunas@cropdesign.com> wrote:
Hello,
I'm trying to run EMBOSS fuzzpro tool, however, I get Illegal character error '_', aparently from the fuzzpro tool itself.
One of the input parameters is amino acid sequence pattern, for instance I submit AV[RL]E, but somehow it get's converted and passed to the fuzzpro as AV__ob__RL__cb__E, and then apparently these '_' are causing the error. I tested the tool on command line and it works fine. Also it works on Galaxy if I submit AVRE (just amino acid letters no special characters for pattern)
So basically seems that in my input pattern string AV[RL]E the character [ is somehow converted into __ob__ and character ] is converted into __cb__
Any ideas how to fix this?
Thanks, Domantas
That would by Galaxy sanitising the "funny" characters, [ and ], and replacing them with __op__ and __cb__ which must be short for open bracket and close bracket. I believe that the fuzzpro tool (and perhaps others) need to have an explicit <sanitizer> and <valid> entry in their Galaxy wrapper XML file to allow these characters though. http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Peter