Hi,

None of the solutions that were mentioned fixed the issue. I will do some more debugging later this evening.

Thanks,
Raj

On Thursday, March 28, 2013 12:26:56 PM, James Taylor wrote:
I haven't looked at this directly, but it should be using None, in
which case the correct comparison is "library_type is None" and
"library_type is not None".

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam <ra...@uga.edu> wrote:
Hello,

I am trying to get the trinity wrapper to work on our local galaxy
installation using the latest trinity version.

The main issue is that the Trinity.pl call has --SS_lib_type None in the
script file. The data I am using is unstranded paired end reads and I am
selecting None in the tool parameters.
I looked at the trinity_all.xml file and it seems like the following code is
not working:

             #if $inputs.library_type != 'None':
                 --SS_lib_type $inputs.library_type
             #end if

I am new to cheeta and python and I am not sure why this code is not
working. Any suggestion on how to go about debugging it?

This is almost certainly a type comparison error, obscured by
the cheetah template language and the parameter proxy classes.
In Python there is a special object None, which is probably what
the library type is using. I would try making this an explicit
comparison of strings (a pattern used in many other wrappers,
e.g. tools/gatk/*.xml):

              #if str($inputs.library_type) != 'None':
                  --SS_lib_type $inputs.library_type
              #end if

Or, this might work too:

              #if $inputs.library_type != None:
                  --SS_lib_type $inputs.library_type
              #end if

(This does seem to be a bug in the trinity wrapper)

Peter
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--
Bio-informatics consultant
QBCG (http://qbcg.uga.edu)
706-542-6092
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