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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to