On Mon, Dec 12, 2011 at 4:34 PM,  <domantas.motieju...@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.

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