you've got an interesting use-case there.
You may want to use either a dataset list (if you only supply rna_n.bam),
or a paired dataset list (rna_n.bam and dna_n.bam).
I would probably implement a conditional, where the user selects either a
dataset list or a paired dataset list.
The output would then be another collection of output files.
Have a look at the test tool folder, and see if any of the tools named
collection_*.xml fits what you would like to do
These two may be a good basis for what you want to achieve:
[this one creates an output collection]
[this one has a conditional to either select a list or a paired list as
Let us know if you need more help!
On 7 June 2016 at 09:50, Marco Tangaro <ma.tang...@gmail.com> wrote:
> Dear experts,
> my name is Marco and I'm working to port our python tool to the Galaxy
> 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
> 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.
> 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,
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