Update Trinity wrapper to correctly handle inputs for genome guided mode

[Hymenium]

Trinity exits immediately if the read files are passed alongside the aligned reads bam file in genome guided mode.

• Problem already identified here: https://help.galaxyproject.org/t/genome-guided-trinity-bug-with-both-fastq-and-bam-files/11771
• The older Trinity 2.9.1+galaxy1 accepts the inputs but does not handle the filenames correctly: Trinity: Bug in output collection when using genome-guided mode #3850
• History to demonstrate issues on some tutorial data, including successful run without genome guided mode and with rnaSPADES using untrusted contigs option: https://usegalaxy.eu/u/hymenium/h/trinity-tests

Changes to trinity.xml seem rather minor, nesting the read data code within the genome guided check. I don't have access to a workstation to run galaxy locally for debugging, but I have suggested some changes in this branch and the tests should still be operational, tools/trinity/trinity.xml

Fixing this bug would also satisfy this request to remove the requirement for read files in genome guided mode:
#3046