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Update JupyTool

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Daniel Blankenberg
2022-03-23 16:42:31 -04:00
parent 62ca0c3424
commit 2216a532b0
1 changed files with 8 additions and 3 deletions
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tools/interactive/interactivetool_jupytool.xml
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</test>
</tests>
<help>
Welcome to the JupyTool! Here you can create, run, and share custom Galaxy tools based upon Jupyter Notebooks.
Welcome to the **JupyTool**! Here you can create, run, and share custom Galaxy tools based upon Jupyter Notebooks.
The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations,
visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization,
@@ -250,8 +250,13 @@ except FileNotFoundError:
do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in Jupyter.
You can start with a new Jupyter notebook from scratch or load an already existing one, e.g. from your colleague and execute it on your dataset.
If you have a defined input dataset you can even execute a Jupyter notebook in a workflow, given that the notebook is writing the output back to the history.
You can specify any number of user-defined inputs using the repeat input, providing `name` value, selecting the type of input, and then providing values.
You can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
You can make the JupyTool reusable in a workflow, by allowing the user to specify input values for the defined input blocks.
Inputs can be accessed by `name` from the automatically provided `GALAXY_INPUTS` dictionary.
Outputs can be written automatically to the user's history by writing to the `outputs` directory for one individual file or to the `outputs/collection` directory for multiple files.
Using collection tools, you can parse out the individual elements from the collection, as needed.
For backwards compatibility, you can import data into the notebook via a predefined `get()` function and write results back to Galaxy with a `put()` function.
</help>
</tool>