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?
Guess we got ~ 2-3 weeks to get the user interface in, it seems doable if there's no too many unexpected things popping up
Some iuc tools are not up to date in usegalaxy.org, this makes some upgrade PR failing, would it be possible to update them (toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1 and toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0). Thanks