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:
script.py -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'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, Marco