New tutorial - single cell data import and format conversion

topics/single-cell/tutorials/EBI-retrieval/tutorial.md

@@ -244,7 +244,7 @@ And the good news is that we can do both those steps using only one tool!
 >
 {: .hands_on}
 
-And that's all! What's even more exciting about the {% icon tool %}) **AnnData Operations** tool is that it automatically calculates a bunch of metrics, such as `log1p_mean_counts`, `log1p_total_counts`, `mean_counts`, `n_cells`, `n_cells_by_counts`, `n_counts`, `pct_dropout_by_counts`, and `total_counts`. Amazing, isn't it?
+And that's all! What's even more exciting about the {% icon tool %} **AnnData Operations** tool is that it automatically calculates a bunch of metrics, such as `log1p_mean_counts`, `log1p_total_counts`, `mean_counts`, `n_cells`, `n_cells_by_counts`, `n_counts`, `pct_dropout_by_counts`, and `total_counts`. Amazing, isn't it?
 
 # Conclusion
 Now you can use this object as input for the [Filter, Plot, Explore tutorial]({% link topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.md %}) and its associated workflow!

topics/single-cell/tutorials/scrna-case_alevin-combine-datasets/tutorial.md

@@ -118,7 +118,7 @@ You can access the data for this tutorial in multiple ways:
 REMEMBER TO ADD THE CODE FOR SNIPPETS BACK IN
 -->
 
-Inspect the {% icon galaxy-eye %} `Experimental Design` text file. This shows you how each `N70X` corresponds to a sample, and whether that sample was from a male or female. This will be important metadata to add to our sample, which we will add very similarly to how you added the `gene_name` and `mito` metadata previously!
+{% icon galaxy-eye %} Inspect the {% icon param-file %} `Experimental Design` text file. This shows you how each `N70X` corresponds to a sample, and whether that sample was from a male or female. This will be important metadata to add to our sample, which we will add very similarly to how you added the `gene_name` and `mito` metadata previously!
 
 # Important tips for easier analysis
 

topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Cell-Data-Set-(CDS)-conversion-test.yml

@@ -0,0 +1,13 @@
+- doc: Test outline for AnnData-to-Cell-Data-Set-(CDS)-conversion
+  job:
+    AnnData:
+      class: File
+      location: https://zenodo.org/record/7053673/files/Mito-counted_AnnData
+      filetype: h5ad
+  outputs:
+    'Inspect AnnData: obs':
+      path: 'test-data/Inspect AnnData: obs.tabular'
+    'Inspect AnnData: X':
+      path: 'test-data/Inspect AnnData: X.tabular'
+    'Inspect AnnData: var':
+      path: 'test-data/Inspect AnnData: var.tabular'

topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Cell-Data-Set-(CDS)-conversion.ga

@@ -0,0 +1 @@
+{"a_galaxy_workflow": "true", "annotation": "AnnData to CDS format conversion (manually using Galaxy buttons). This workflow does not include renaming the column containing gene symbols. ", "creator": [{"class": "Person", "identifier": "0009-0001-2017-8805", "name": "Julia Jakiela"}], "format-version": "0.1", "license": "CC-BY-4.0", "name": "AnnData to Cell Data Set (CDS) conversion", "steps": {"0": {"annotation": "Input file in AnnData format", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [{"description": "Input file in AnnData format", "name": "AnnData"}], "label": "AnnData", "name": "Input dataset", "outputs": [], "position": {"left": 0, "top": 0}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "803b5429-24a8-4ba8-b9f0-d9012a23d190", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", "errors": null, "id": 1, "input_connections": {"input": {"id": 0, "output_name": "output"}}, "inputs": [], "label": null, "name": "Inspect AnnData", "outputs": [{"name": 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topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Seurat-conversion-test.yml

@@ -0,0 +1,11 @@
+- doc: Test outline for AnnData-to-Seurat-conversion
+  job:
+    AnnData:
+      class: File
+      location: https://zenodo.org/record/7053673/files/Mito-counted_AnnData
+      filetype: h5ad
+  outputs:
+    'Inspect AnnData: obs':
+      path: 'test-data/Inspect AnnData: obs.tabular'
+    'Inspect AnnData: X':
+      path: 'test-data/Inspect AnnData: X.tabular'

topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-Seurat-conversion.ga

@@ -0,0 +1 @@
+{"a_galaxy_workflow": "true", "annotation": "AnnData to Seurat format conversion (manually using Galaxy buttons)", "creator": [{"class": "Person", "identifier": "0009-0001-2017-8805", "name": "Julia Jakiela"}, {"class": "Person", "identifier": "0009-0008-9422-6380", "name": "Morgan Howells"}], "format-version": "0.1", "license": "CC-BY-4.0", "name": "AnnData to Seurat conversion", "steps": {"0": {"annotation": "Input file in AnnData format", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [{"description": "Input file in AnnData format", "name": "AnnData"}], "label": "AnnData", "name": "Input dataset", "outputs": [], "position": {"left": 0.0, "top": 0.0}, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "f783e6c3-808c-4dd2-84dd-6130c8230970", "when": null, "workflow_outputs": []}, "1": {"annotation": "", "content_id": 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topics/single-cell/tutorials/scrna-data-ingest/workflows/AnnData-to-SingleCellExperiment-(SCE)-conversion-test.yml

@@ -0,0 +1,12 @@
+- doc: Test outline for AnnData-to-SingleCellExperiment-(SCE)-conversion
+  job:
+    AnnData:
+      class: File
+      location: https://zenodo.org/record/7053673/files/Mito-counted_AnnData
+      filetype: h5ad
+    Cell ID column: index
+  outputs:
+    'Inspect AnnData: obs':
+      path: 'test-data/Inspect AnnData: obs.tabular'
+    'Inspect AnnData: X':
+      path: 'test-data/Inspect AnnData: X.tabular'