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?


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