If I understand the goal correctly, please see the items below to aid with batch analysis.
- Dataset collections: Simple through complex data structures that can optionally include extended metadata to keep an analysis organized.
Workflows and Sub-workflows: Analysis "recipes". Allows one to set the inputs once (at the start) and launch a full analysis pipeline in one step.
Galaxy API: Run Galaxy analysis line-command, by itself, or as part of a larger computational/data management strategy. All Galaxy results will still be available in the GUI, should you choose to host/share the web server.
The Galaxy ecosystem: https://galaxyproject.github.io/
Thanks! Jen, Galaxy team