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.cock@googlemail.com> wrote:
On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam <raj76@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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