Is it possible to use loops (or cycles) in Galaxy workflow? I have a file with multiple fasta sequences and I need to process them one-by-one with a Galaxy tool (e.g. EMBOSS cusp tool). The tool normally just allows to process all sequences together (concatenated).
loops are currently not possible, but the Galaxy Team is actively working on that. Dataset collections, currently scheduled for the next Galaxy release in one month, will address your use case I think.
In the meantime try to insert the following snipped into your emboss tool.
<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1" merge_outputs="TODO"></parallelism>
Adopt the split_inputs and merge_outputs to the variables in your emboss wrapper. The snippet will automatically split your multi FASTA file into simgle FASTA files and concatenate the output of all runs into one single output. The only requirement is that the outputs can be concatenated.