Dear experts,
my name is Marco and I'm working to port our python tool to the Galaxy framework.
The main script needs a rna.bam file as input, a reference fasta file, both mandatory. Finally, you can add a dna.bam file, but this is optional.
Therefore an example command is: -i rna.bam -f reference.fa -j dna.bam

The outout is a tabular.
Again the -j dna.bam option is completely optional.
So quite soon it turned out that I had to use a python wrapper to parse our script. Now the wrapper works fine.

The next step is to run the tool over multiple input file and we would like to avoid to use a workflow.

The idea is that to each input file corresponds an output file. The reference is still the same.
For instance, we have:

rna_1.bam + dna_1.bam -> output_1.txt
rna_2.bam + dna_2.bam -> output_2.txt
rna_3.bam + dna_3.bam -> output_3.txt
and so on.

But I don't know the best strategy to give to my wrapper multiple input files.
Moreover I have to be sure, when the dna_xyz.bam files are uploaded, that they correspond to the right rna_xyz.bam file.

I would like to have as output a page which is showing as results the link to the single output files as suggested here.
planning to integrate a javascript interface.

I've browsed a lot, but on multiple input file the posts are old.
I'm using the last galaxy release (16_04).

I'm quite new to the galaxy world...
Thanks a lot for your suggestions,