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)

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