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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
