full_melanoma_without_scaling_xenium_workflow

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flowchart TD
  0["ℹ️ Input Dataset\nmelanoma_roi.spatialdata.zip"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["initial Anndata table"];
  0 -->|output| 1;
  2["Inspect AnnData"];
  1 -->|result_adata| 2;
  3["Inspect AnnData"];
  1 -->|result_adata| 3;
  4["QC metrics before filtering"];
  1 -->|result_adata| 4;
  480e466a-0f38-40d8-a144-9544b85e7bf0["Output\nQC metrics before filtering"];
  4 --> 480e466a-0f38-40d8-a144-9544b85e7bf0;
  style 480e466a-0f38-40d8-a144-9544b85e7bf0 stroke:#2c3143,stroke-width:4px;
  5["Violin_Plots_before_filteration"];
  4 -->|anndata_out| 5;
  a0abc5c3-707e-45b4-9004-b319c5a8b9d7["Output\nViolin_Plots_before_filteration"];
  5 --> a0abc5c3-707e-45b4-9004-b319c5a8b9d7;
  style a0abc5c3-707e-45b4-9004-b319c5a8b9d7 stroke:#2c3143,stroke-width:4px;
  6["Scatter plot before filtering"];
  4 -->|anndata_out| 6;
  68b0cadd-79b3-436a-b8ef-ff785b7b2659["Output\nScatter plot before filtering"];
  6 --> 68b0cadd-79b3-436a-b8ef-ff785b7b2659;
  style 68b0cadd-79b3-436a-b8ef-ff785b7b2659 stroke:#2c3143,stroke-width:4px;
  7["SpatialData with QC metrics"];
  0 -->|output| 7;
  4 -->|anndata_out| 7;
  8["Scanpy filter Minimum genes expressed"];
  4 -->|anndata_out| 8;
  47b83004-9657-421f-af26-fff91e232ff2["Output\nFilter minimum genes expressed"];
  8 --> 47b83004-9657-421f-af26-fff91e232ff2;
  style 47b83004-9657-421f-af26-fff91e232ff2 stroke:#2c3143,stroke-width:4px;
  9["Spatial Plot total_counts before filtering"];
  7 -->|spatialdata_output| 9;
  0d65f539-3c53-4486-bf86-34446d2f0130["Output\nSpatial Plot total_counts before filtering"];
  9 --> 0d65f539-3c53-4486-bf86-34446d2f0130;
  style 0d65f539-3c53-4486-bf86-34446d2f0130 stroke:#2c3143,stroke-width:4px;
  10["Spatial Plot n_genes_by_counts before filtering"];
  7 -->|spatialdata_output| 10;
  7efe5b5c-cef3-4d16-b7b3-ad219e5f308b["Output\nSpatial Plot n_genes_by_counts before filtering"];
  10 --> 7efe5b5c-cef3-4d16-b7b3-ad219e5f308b;
  style 7efe5b5c-cef3-4d16-b7b3-ad219e5f308b stroke:#2c3143,stroke-width:4px;
  11["Inspect AnnData"];
  8 -->|anndata_out| 11;
  12["Filter minimum number of counts of gene expressed"];
  8 -->|anndata_out| 12;
  3eeec312-343d-45dc-861e-8b2897774a73["Output\nFilter minimum number of counts of gene expressed"];
  12 --> 3eeec312-343d-45dc-861e-8b2897774a73;
  style 3eeec312-343d-45dc-861e-8b2897774a73 stroke:#2c3143,stroke-width:4px;
  13["Inspect AnnData"];
  12 -->|anndata_out| 13;
  14["Filter minimum number of cells expressed"];
  12 -->|anndata_out| 14;
  b7fd86f9-614c-40e7-bcfe-adf512b7d8f8["Output\nFilter minimum number of cells expressed"];
  14 --> b7fd86f9-614c-40e7-bcfe-adf512b7d8f8;
  style b7fd86f9-614c-40e7-bcfe-adf512b7d8f8 stroke:#2c3143,stroke-width:4px;
  15["Filter genes based on number of cells or counts Minimum number of counts"];
  14 -->|anndata_out| 15;
  b94fe64d-2fc6-4f03-8fe4-bd912045d7e2["Output\nFilter genes based on number of cells or counts Minimum number of counts"];
  15 --> b94fe64d-2fc6-4f03-8fe4-bd912045d7e2;
  style b94fe64d-2fc6-4f03-8fe4-bd912045d7e2 stroke:#2c3143,stroke-width:4px;
  16["Inspect AnnData"];
  15 -->|anndata_out| 16;
  17["Filter maximum number of counts"];
  15 -->|anndata_out| 17;
  cda1adb3-249e-4c41-9964-c7108943e2c1["Output\nFilter maximum number of counts"];
  17 --> cda1adb3-249e-4c41-9964-c7108943e2c1;
  style cda1adb3-249e-4c41-9964-c7108943e2c1 stroke:#2c3143,stroke-width:4px;
  18["Filter maximum number of genes expressed"];
  17 -->|anndata_out| 18;
  17e8e16f-fba2-449e-ad0c-c12df7691a94["Output\nFilter maximum number of genes expressed"];
  18 --> 17e8e16f-fba2-449e-ad0c-c12df7691a94;
  style 17e8e16f-fba2-449e-ad0c-c12df7691a94 stroke:#2c3143,stroke-width:4px;
  19["Inspect AnnData"];
  18 -->|anndata_out| 19;
  20["Filter cell_area more than 10"];
  18 -->|anndata_out| 20;
  acc71f7e-f132-4bd2-9e53-877e8770171b["Output\nFilter cell_area more than 10"];
  20 --> acc71f7e-f132-4bd2-9e53-877e8770171b;
  style acc71f7e-f132-4bd2-9e53-877e8770171b stroke:#2c3143,stroke-width:4px;
  21["Filter cell_area less than 400"];
  20 -->|anndata_out| 21;
  ca03e483-8b0f-44cb-b3ae-e15689b6f2c3["Output\nFilter cell_area less than 400"];
  21 --> ca03e483-8b0f-44cb-b3ae-e15689b6f2c3;
  style ca03e483-8b0f-44cb-b3ae-e15689b6f2c3 stroke:#2c3143,stroke-width:4px;
  22["Filtered AnnData table"];
  21 -->|anndata_out| 22;
  60870001-3a7c-4fbb-ab6b-970421fd652e["Output\nFiltered AnnData table"];
  22 --> 60870001-3a7c-4fbb-ab6b-970421fd652e;
  style 60870001-3a7c-4fbb-ab6b-970421fd652e stroke:#2c3143,stroke-width:4px;
  23["Violin_Plots_after_filteration"];
  22 -->|anndata_out| 23;
  a0cf61fc-3975-4710-aa0e-e9f5692f8776["Output\nViolin_Plots_after_filteration"];
  23 --> a0cf61fc-3975-4710-aa0e-e9f5692f8776;
  style a0cf61fc-3975-4710-aa0e-e9f5692f8776 stroke:#2c3143,stroke-width:4px;
  24["Filtered AnnData with counts layer"];
  22 -->|anndata_out| 24;
  22 -->|anndata_out| 24;
  a055e10c-0d99-425e-9c28-d63f06c82aef["Output\nFiltered AnnData with counts layer"];
  24 --> a055e10c-0d99-425e-9c28-d63f06c82aef;
  style a055e10c-0d99-425e-9c28-d63f06c82aef stroke:#2c3143,stroke-width:4px;
  25["Scatter plot after filtering"];
  22 -->|anndata_out| 25;
  7bca78a9-9ce9-4ec4-9780-edb169e1f0a8["Output\nScatter plot after filtering"];
  25 --> 7bca78a9-9ce9-4ec4-9780-edb169e1f0a8;
  style 7bca78a9-9ce9-4ec4-9780-edb169e1f0a8 stroke:#2c3143,stroke-width:4px;
  26["SpatialData Operations"];
  0 -->|output| 26;
  22 -->|anndata_out| 26;
  27["Normalised AnnData"];
  22 -->|anndata_out| 27;
  c6a7a260-bf51-4d43-bd09-ec330f7b2401["Output\nNormalised AnnData"];
  27 --> c6a7a260-bf51-4d43-bd09-ec330f7b2401;
  style c6a7a260-bf51-4d43-bd09-ec330f7b2401 stroke:#2c3143,stroke-width:4px;
  28["Spatial Plot total_counts after filtering"];
  26 -->|spatialdata_output| 28;
  53ce37a0-b4b7-4cae-815e-7d559f9ffbcc["Output\nSpatial Plot after filtering"];
  28 --> 53ce37a0-b4b7-4cae-815e-7d559f9ffbcc;
  style 53ce37a0-b4b7-4cae-815e-7d559f9ffbcc stroke:#2c3143,stroke-width:4px;
  29["Spatial Plot table_processed after filtering"];
  26 -->|spatialdata_output| 29;
  7bca9117-c8ca-4e90-9460-6654be842c12["Output\nSpatial Plot table_processed after filtering"];
  29 --> 7bca9117-c8ca-4e90-9460-6654be842c12;
  style 7bca9117-c8ca-4e90-9460-6654be842c12 stroke:#2c3143,stroke-width:4px;
  30["Log-normalised AnnData"];
  27 -->|anndata_out| 30;
  660d8a75-9957-43e7-960c-135063391fbe["Output\nLog-normalised AnnData"];
  30 --> 660d8a75-9957-43e7-960c-135063391fbe;
  style 660d8a75-9957-43e7-960c-135063391fbe stroke:#2c3143,stroke-width:4px;
  31["AnnData with HVGs"];
  30 -->|anndata_out| 31;
  4740d7e3-1cd9-4b76-8370-0e70499cb489["Output\nAnnData with HVGs"];
  31 --> 4740d7e3-1cd9-4b76-8370-0e70499cb489;
  style 4740d7e3-1cd9-4b76-8370-0e70499cb489 stroke:#2c3143,stroke-width:4px;
  32["Plot HVGs"];
  31 -->|anndata_out| 32;
  a3d8a78b-9a07-4a6a-91bb-70e9e8212b71["Output\nPlot HVGs"];
  32 --> a3d8a78b-9a07-4a6a-91bb-70e9e8212b71;
  style a3d8a78b-9a07-4a6a-91bb-70e9e8212b71 stroke:#2c3143,stroke-width:4px;
  33["AnnData with PCA"];
  31 -->|anndata_out| 33;
  8efe9097-9ad1-45ee-a143-11de4e3842c2["Output\nAnnData with PCA"];
  33 --> 8efe9097-9ad1-45ee-a143-11de4e3842c2;
  style 8efe9097-9ad1-45ee-a143-11de4e3842c2 stroke:#2c3143,stroke-width:4px;
  34["Compute a neighborhood graph of observations"];
  33 -->|anndata_out| 34;
  c687c794-9ec8-40a5-94c4-0b03f3342ee2["Output\nCompute a neighborhood graph of observations"];
  34 --> c687c794-9ec8-40a5-94c4-0b03f3342ee2;
  style c687c794-9ec8-40a5-94c4-0b03f3342ee2 stroke:#2c3143,stroke-width:4px;
  35["Plot PCA"];
  33 -->|anndata_out| 35;
  e27e7111-88e7-47d9-87be-e301065d75ec["Output\nPlot PCA"];
  35 --> e27e7111-88e7-47d9-87be-e301065d75ec;
  style e27e7111-88e7-47d9-87be-e301065d75ec stroke:#2c3143,stroke-width:4px;
  36["AnnData with UMAP"];
  34 -->|anndata_out| 36;
  afbad56e-b458-42f7-afb5-0b8e67650a10["Output\nAnnData with UMAP"];
  36 --> afbad56e-b458-42f7-afb5-0b8e67650a10;
  style afbad56e-b458-42f7-afb5-0b8e67650a10 stroke:#2c3143,stroke-width:4px;
  37["Plot  UMAP"];
  36 -->|anndata_out| 37;
  dc45eb7a-5163-4398-b5c8-ef8adeffee18["Output\nPlot UMAP"];
  37 --> dc45eb7a-5163-4398-b5c8-ef8adeffee18;
  style dc45eb7a-5163-4398-b5c8-ef8adeffee18 stroke:#2c3143,stroke-width:4px;
  38["Anndata with leiden_res_0.2"];
  36 -->|anndata_out| 38;
  e3b4870a-92a7-4bd0-b9c5-e2a56be63007["Output\nAnndata with leiden_res_0.2"];
  38 --> e3b4870a-92a7-4bd0-b9c5-e2a56be63007;
  style e3b4870a-92a7-4bd0-b9c5-e2a56be63007 stroke:#2c3143,stroke-width:4px;
  39["AnnData with Leiden comparison 0.2 and 0.4"];
  38 -->|anndata_out| 39;
  5d8af959-556a-4f34-8653-328d44d4728b["Output\nAnnData with Leiden comparison 0.2 and 0.4"];
  39 --> 5d8af959-556a-4f34-8653-328d44d4728b;
  style 5d8af959-556a-4f34-8653-328d44d4728b stroke:#2c3143,stroke-width:4px;
  40["AnnData with Leiden comparison 0.2 and 0.4 and 0.6"];
  39 -->|anndata_out| 40;
  9cdc369f-fb6e-4a35-aec3-99eb7342b9c3["Output\nAnnData with Leiden comparison 0.2 and 0.4 and 0.6"];
  40 --> 9cdc369f-fb6e-4a35-aec3-99eb7342b9c3;
  style 9cdc369f-fb6e-4a35-aec3-99eb7342b9c3 stroke:#2c3143,stroke-width:4px;
  41["Plot Leiden comparison"];
  40 -->|anndata_out| 41;
  263c895d-0bc7-4d53-853b-675fc0876fb9["Output\nPlot Leiden comparison"];
  41 --> 263c895d-0bc7-4d53-853b-675fc0876fb9;
  style 263c895d-0bc7-4d53-853b-675fc0876fb9 stroke:#2c3143,stroke-width:4px;
  42["Rank genes for characterizing groups"];
  40 -->|anndata_out| 42;
  de26d617-2bf2-4470-894c-de70fd813cf5["Output\nAnnData with markers"];
  42 --> de26d617-2bf2-4470-894c-de70fd813cf5;
  style de26d617-2bf2-4470-894c-de70fd813cf5 stroke:#2c3143,stroke-width:4px;
  89b1795e-0238-4835-b5a9-1a1d40ba4f7e["Output\nRank genes for characterizing groups"];
  42 --> 89b1795e-0238-4835-b5a9-1a1d40ba4f7e;
  style 89b1795e-0238-4835-b5a9-1a1d40ba4f7e stroke:#2c3143,stroke-width:4px;
  43["Plot ranking of genes"];
  42 -->|anndata_out| 43;
  18d96a8b-501e-47bb-ab29-f9b09e353b8a["Output\nPlot ranking of genes"];
  43 --> 18d96a8b-501e-47bb-ab29-f9b09e353b8a;
  style 18d96a8b-501e-47bb-ab29-f9b09e353b8a stroke:#2c3143,stroke-width:4px;
  44["AnnData with spatial neighbours"];
  42 -->|anndata_out| 44;
  aafb91c5-c8d4-4876-88df-9732f4096a6b["Output\nAnnData with spatial neighbours"];
  44 --> aafb91c5-c8d4-4876-88df-9732f4096a6b;
  style aafb91c5-c8d4-4876-88df-9732f4096a6b stroke:#2c3143,stroke-width:4px;
  45["Squidpy"];
  44 -->|spatialdata_output_h5ad| 45;
  46["Squidpy"];
  45 -->|spatialdata_output_h5ad| 46;
  47["Squidpy Plot"];
  45 -->|spatialdata_output_h5ad| 47;
  53fde591-e03f-43c4-a934-de1179115d79["Output\nPlot Centrality Scores"];
  47 --> 53fde591-e03f-43c4-a934-de1179115d79;
  style 53fde591-e03f-43c4-a934-de1179115d79 stroke:#2c3143,stroke-width:4px;
  48["Squidpy Plot"];
  46 -->|spatialdata_output_h5ad| 48;
  f3ad4b94-c4f7-4ee1-8da9-28e5a62a43a0["Output\nPlot Neighborhood Enrichment"];
  48 --> f3ad4b94-c4f7-4ee1-8da9-28e5a62a43a0;
  style f3ad4b94-c4f7-4ee1-8da9-28e5a62a43a0 stroke:#2c3143,stroke-width:4px;
  49["AnnData with Squidpy results"];
  46 -->|spatialdata_output_h5ad| 49;
  6b0b214b-c790-4c5c-ae8f-ea7bbbba77e0["Output\nAnnData with Squidpy results"];
  49 --> 6b0b214b-c790-4c5c-ae8f-ea7bbbba77e0;
  style 6b0b214b-c790-4c5c-ae8f-ea7bbbba77e0 stroke:#2c3143,stroke-width:4px;
  50["CellTypist-annotated AnnData"];
  49 -->|spatialdata_output_h5ad| 50;
  be8d4eb6-9c98-4b47-8ef5-57acb4348dd1["Output\nCellTypist-annotated AnnData"];
  50 --> be8d4eb6-9c98-4b47-8ef5-57acb4348dd1;
  style be8d4eb6-9c98-4b47-8ef5-57acb4348dd1 stroke:#2c3143,stroke-width:4px;
  1a8734e4-565a-48b7-879d-83fe9f0f77e1["Output\nPlot CellTypist"];
  50 --> 1a8734e4-565a-48b7-879d-83fe9f0f77e1;
  style 1a8734e4-565a-48b7-879d-83fe9f0f77e1 stroke:#2c3143,stroke-width:4px;
  51["SpatialData with Squidpy results"];
  0 -->|output| 51;
  49 -->|spatialdata_output_h5ad| 51;
  52["Final Lana Anndata"];
  50 -->|anndata_out| 52;
  ffad758d-6eb9-4ec0-8b05-615c6e27f772["Output\nFinal Liana Anndata"];
  52 --> ffad758d-6eb9-4ec0-8b05-615c6e27f772;
  style ffad758d-6eb9-4ec0-8b05-615c6e27f772 stroke:#2c3143,stroke-width:4px;
  53["Spatial_Plot_on_VGF_morons_HVG"];
  51 -->|spatialdata_output| 53;
  d3883ba5-bbbb-4cb8-9678-22bd1b7b2f6b["Output\nSpatial_Plot_on_VGF_morons_HVG"];
  53 --> d3883ba5-bbbb-4cb8-9678-22bd1b7b2f6b;
  style d3883ba5-bbbb-4cb8-9678-22bd1b7b2f6b stroke:#2c3143,stroke-width:4px;
  54["SpatialData with Final metrics"];
  0 -->|output| 54;
  52 -->|anndata_out| 54;
  55["SpatialData Plot"];
  54 -->|spatialdata_output| 55;
  95aaccc1-d99d-44bf-a4b9-d0dbfacff685["Output\nPlot spatial clusters"];
  55 --> 95aaccc1-d99d-44bf-a4b9-d0dbfacff685;
  style 95aaccc1-d99d-44bf-a4b9-d0dbfacff685 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. Provide your workflow
   • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
   • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/spatial-melanoma-SPICA/workflows/full-melanoma-without-scaling-xenium-workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows