I am currently facing the following issue: I have a tool (https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/vapor/vapor/1.0.2+galaxy2) that expects a multi-sequence FASTA file and, in my case, a list of PE data (representing different samples. The tool will then find the fasta sequence that best matches the reads in each input and will produce a results collection equal in number of elements to the number of PE input samples. So far, so good. Now, however, I would like to extend this to a collection of multisequence fastas, and I want a run of each sample against each such fasta resulting in a nested list with e.g. samples as the elements of the outer list and assigned best match for that sample for each of the multi-sequence Fastas.
After many attempts I'm about to conclude that there's no elegant way to achieve this, but maybe I'm wrong?
The only rather stupid-looking solution I have is to extract, as part of a workflow, each multi-sequence fasta (it's always eight of them) with __EXTRACT_DATASET__, then run vapor on each of those datasets and the list:paired collection.
IIRC we do support that in the backend, but haven't enabled this for lack of a user interface. Just to be sure, can you share a history with your workaround ? I wonder if this could also be done by nesting your collection deeper
hey workflow gurus! staramr specifies species using a drop down (this is necessary to run PointFinder) - while the user could set this by changing the "default tool parameters" at pipeline invocation time, is there any way to ask for a user input parameter for the pipeline (so it shows up right at the top like other pipeline inputs) and connect this to the dropdown?