https://github.com/trinityrnaseq/trinityrnaseq/wiki/SuperTranscripts I read here that there is a utility within galaxy to allow me to assemble a SuperTranscript since I am working with RNAseq data from a non-model organism and no reference genome. I can't find any tools within galaxy to help me create this.
It seems to be an easy galaxy tool to write. The best would be to add it at https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity No promise, but I'll try to do it if I find some time soon
This Trinity utility has not been wrapped for Galaxy in the ToolShed: https://usegalaxy.org/toolshed/
I would suggest trying the public Galaxy that the authors recommend. If it is not there, you could ask the tool authors if there are plans to wrapped/add this to a public Galaxy and/or wrap it in the ToolShed for use in your own local/cloud/docker Galaxy server. https://github.com/trinityrnaseq/trinityrnaseq/wiki/Accessing-Trinity-on-Publicly-Available-Compute-Resources
It may be that it is only available line command. Instructions are on the same wiki above and they can help with troubleshooting as needed.
I also asked the IUC developers if there are any plans for this in future development. Please follow or join in on the question at Gitter here: https://gitter.im/galaxy-iuc/iuc?at=5b19a05d106f3c24bde286e6
Thanks! Jen, Galaxy team