From 2216a532b0ba60af0126a67c34d52497eaf0b20e Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Wed, 23 Mar 2022 16:42:31 -0400 Subject: [PATCH] Update JupyTool --- tools/interactive/interactivetool_jupytool.xml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/tools/interactive/interactivetool_jupytool.xml b/tools/interactive/interactivetool_jupytool.xml index 01c3cd26366..b719692f79c 100644 --- a/tools/interactive/interactivetool_jupytool.xml +++ b/tools/interactive/interactivetool_jupytool.xml @@ -240,7 +240,7 @@ except FileNotFoundError: - 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.