Full tool name:
Convert Kraken data to Galaxy taxonomy representation
You’ll need to use the same version of all the
Kraken tools in the same analysis. This includes the Data Manager (that creates the associated indexes).
In short, avoid the
Kraken2 version of all upstream tools until the DM is ready or problems can come up.
@dfornika I could be missing something here, or this is part of a work-in-progress, or known issue, or something we need to ticket. From what I can tell “Convert Kraken data to Galaxy taxonomy representation” (tool id “Kraken2tax”) only has one version in the ToolShed, and it is older (2017). It will access Kraken indexes. Not sure if it is expected to list both Kraken and Kraken2 indexes once the Kraken2 DM is finalized/used. Or, if there will be a new version of the tool for that functionality (one for Kraken, one for Kraken2). However done, the form(s) should point to the correct indexes based on the upstream tool version. The current short tool name is a bit confusing but not much can be done about that (“Kraken2tax” means “Kraken-TO-taxonomy”). Maybe there will be a Kraken22tax with a new tool name like “Convert Kraken2 data to Galaxy taxonomy representation” or some reorganization at the data table level for the existing Kraken2tax so that it captures all indexes?
Also pinged @dfornika at the IUC tool development forum here: https://gitter.im/galaxy-iuc/iuc?at=5cd99ee58fcdb05d47ccbcd5