mapping and de novo assembly of plant without reference genome
You have multiple questions, I will try to answer one by one:


On creating an index with STAR: As long as you provide a fasta file and its corresponding gff, you will be able to generate an index.
On creating a reference with Trinity: You have mentioned "to construct the Reference Genome with Trinity", however, with your RNA-seq data and Trinity, you can construct a de novo transcriptome and not a genome.
Uploading files to Galaxy: I suggest to do so via FTP using FileZilla or something similar. The transfer can take some time if your files are large though.


If I understand your questions correctly, you are performing RNA-seq and you are concerned about the completeness of the genome of your model organism. In that case, I would advise to bring together a de novo transcriptome from your RNA-seq data (with Trinity), use one of the quasi-mapping methods (with a tool like Salmon or kallisto).