Thanks Peter,
added <sanitizer> tag to original fuzzypro's
xml wrapper based on your suggestion and now it works.
(Hmm probably this should be done for some
other EMBOSS wrappers, also for other "funny"
characters that appear in pattern definitions)
from emobss_fuzzypro.xml
...
<param name="pattern" size="30"
type="text" value="">
Re: [galaxy-user] EMBOSS fuzzpro tool
pattern is not read correctly from the input
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.