I made an R script in Jupyter that makes plots and datasets, how do I tell the tool using this notebook to send outputted dataset A to input A of the next tool ?
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Hi @jean.le-cras, welcome to GalaxyHelp!
You can export the saved datasets from R to your Galaxy history. Then you can use the exported datasets from the history as inputs to other Galaxy tools.
Please check out this section of the tutorial to learn more about interacting from R to Galaxy: Hands-on: RStudio in Galaxy / RStudio in Galaxy / Using Galaxy and Managing your Data
Best,
Pavan
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I can surely do this way manually, but if the next tool isn’t an interactive jupyterLab how do I that (EcoMap in my case)?
You will be exporting the data out of the interactive environment back into the Galaxy history. The tutorial @pavanvidem shared explains how to do this with the gx_put() command.
More tutorials → GTN Materials Search (query=jupyter)
Once the data is in your history, double check the assigned datatype and modifying as needed. For this tool you will need the datatype format tabular. Your data is likely already in this format but double check that Galaxy detected that format and change it if needed. → FAQ: Changing the datatype
Screenshot of where to review the expected input format. The data for regular tools in the tool panel is always sourced from the Galaxy history (even if loaded by URL at runtime into the history).
Please give this a try! Thanks! 
Thanks you @jennaj and @pavanvidem for the solution. My issue was more specific, my Jupyter notebook produces dataframes and plots so I have to put all the outputted files in “outputs/collection” directory and a maximum of one file in “outputs” directory. If I want to pass a file to only one other tool I can put this file in “outputs” and give it the correct datatype format, otherwise if I want to pass multiple files to multiple tools I would need an intermediary step that splits the collection like filter collection.
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