diff --git a/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md b/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md index 8d6287dbfca64e..6e8980bb515cdc 100644 --- a/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md +++ b/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/tutorial.md @@ -64,27 +64,29 @@ To start, let's get our dataset loaded into Galaxy. {% include _includes/cyoa-choices.html option1='EBI Data Retrieval' option2='Importing from a history' option3='Uploading from Zenodo' default='EBI Data Retrieval' text="There are multiple ways in which to collect the data for this tutorial. I find it easiest to do so via the EBI Data Retrieval." %} -
-## **EBI Data Retrieval** -You may retrieve that files necessary to construct a Seurat Object in this way. Doing to will alleviate the necessity to convert AnnData (Python) objects into Seurat (R) objects: -> GetData +
+> EBI Data Retrieval +> +> You may retrieve that files necessary to construct a Seurat Object in this way. Doing to will alleviate the necessity to convert AnnData (Python) objects into Seurat (R) objects: > > Run{% tool [EBI SCXA Data Retrieval](toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2) %} with the following parameters: > - *"SC-Atlas experiment accession"*: `E-MTAB-6945` > - *"Choose the type of matrix to download"*: `Raw filtered counts` {: .hands_on}
-
-## **Importing from a history** -You can import [this history](https://singlecell.usegalaxy.eu/u/camila-goclowski/h/tool-based-seurat-fpe-input-data) - -{% snippet faqs/galaxy/histories_import.md %} -This also alleviates the necessity to convert the AnnData object into a Seurat one, which is an additional step you must complete if you choose to use the next method. +
+> Importing from a history +> You can import [this history](https://singlecell.usegalaxy.eu/u/camila-goclowski/h/tool-based-seurat-fpe-input-data) +> +> {% snippet faqs/galaxy/histories_import.md %} +> +> This also alleviates the necessity to convert the AnnData object into a Seurat one, which is an additional step you must complete if you choose to use the next method. +{:.hands_on}
-
-## **Uploading from Zenodo** -> Option 3: Uploading from Zenodo + +
+> Uploading from Zenodo > > 1. Create a new history for this tutorial > 2. Import the AnnData object from [Zenodo]({{ page.zenodo_link }})