There are quite a few published workflows available for RNAseq under Shared data --> Workflows on: useGalaxy.org.
Among these workflows is this reference based transcriptome profiling one (https://usegalaxy.org/u/biocrusoe/w/rnaseq-reference-based-by-nekrut) that has an extensive tutorial associated with it (https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq).
You can import any of the published workflows to your personal Galaxy account and modify the parameters (and even the tools used) in the workflow editor.
After you have completed your differential expression analysis you can look specifically at your long non-coding RNAs. I would recommend using a reference transcriptome that has annotations for protein-coding and non-coding transcripts, such as Ensembl or RefSeq.
Mo Heydarian, Galaxy Team