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="">

      <sanitizer>
          <valid>
            <add value="["/>
            <add value="]"/>
          </valid>
      </sanitizer>

      <label>Search pattern</label>
</param>
...

Domantas



From:
Peter Cock <p.j.a.c...@googlemail.com>
To:
domantas.motieju...@cropdesign.com
Cc:
galaxy-user@lists.bx.psu.edu
Date:
12/12/2011 05:41 PM
Subject:
Re: [galaxy-user] EMBOSS fuzzpro tool pattern is not read correctly from 
the input



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.
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

Peter

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