AnnData object to Monocle input files

Run Workflow in Galaxy

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• Galaxy Europe
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nAnnData to extract genes & cells annotations"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nAnnData before processing to extract clean expression matrix"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Extract cell annotations"];
  0 -->|output| 2;
  9d66a217-4269-4fb4-9a4e-520eedbb0c9d["Output\nExtracted cell annotations (obs)"];
  2 --> 9d66a217-4269-4fb4-9a4e-520eedbb0c9d;
  style 9d66a217-4269-4fb4-9a4e-520eedbb0c9d stroke:#2c3143,stroke-width:4px;
  3["Extract gene annotations"];
  0 -->|output| 3;
  03537e97-d668-4ce2-ba6b-2952a18a2752["Output\nExtracted gene annotations (var)"];
  3 --> 03537e97-d668-4ce2-ba6b-2952a18a2752;
  style 03537e97-d668-4ce2-ba6b-2952a18a2752 stroke:#2c3143,stroke-width:4px;
  4["Extract clean expression matrix"];
  1 -->|output| 4;
  963462c8-4ae0-486c-8173-d98339127850["Output\nUnprocessed expression matrix"];
  4 --> 963462c8-4ae0-486c-8173-d98339127850;
  style 963462c8-4ae0-486c-8173-d98339127850 stroke:#2c3143,stroke-width:4px;
  5["Filter out unwanted cell types"];
  2 -->|obs| 5;
  5dcb7029-8d03-445d-bb3e-a3119e502be4["Output\nCells without macrophages"];
  5 --> 5dcb7029-8d03-445d-bb3e-a3119e502be4;
  style 5dcb7029-8d03-445d-bb3e-a3119e502be4 stroke:#2c3143,stroke-width:4px;
  6["gene_short_name annotation"];
  3 -->|var| 6;
  15fd415b-2d73-4a1d-92ad-200bb2e73853["Output\nGenes table with gene_short_name colname"];
  6 --> 15fd415b-2d73-4a1d-92ad-200bb2e73853;
  style 15fd415b-2d73-4a1d-92ad-200bb2e73853 stroke:#2c3143,stroke-width:4px;
  7["Cut cells IDs"];
  5 -->|out_file1| 7;
  f9bde249-43b9-4424-8285-e437549223e2["Output\nFiltered cells IDs "];
  7 --> f9bde249-43b9-4424-8285-e437549223e2;
  style f9bde249-43b9-4424-8285-e437549223e2 stroke:#2c3143,stroke-width:4px;
  8["Cut genes IDs"];
  6 -->|out_file1| 8;
  b22efa1d-db99-435f-9357-74150ac9a437["Output\nGenes IDs"];
  8 --> b22efa1d-db99-435f-9357-74150ac9a437;
  style b22efa1d-db99-435f-9357-74150ac9a437 stroke:#2c3143,stroke-width:4px;
  9["Filter matrix by cells"];
  7 -->|out_file1| 9;
  4 -->|X| 9;
  b45f18b6-e385-41a1-a8f0-f94e6616e2b3["Output\nPre-filtered matrix (by cells)"];
  9 --> b45f18b6-e385-41a1-a8f0-f94e6616e2b3;
  style b45f18b6-e385-41a1-a8f0-f94e6616e2b3 stroke:#2c3143,stroke-width:4px;
  10["Remove duplicate column cells IDs"];
  9 -->|out_file1| 10;
  f4d6a581-9b42-41dc-9a4a-278fe5d6591c["Output\nFiltered matrix (by cells) "];
  10 --> f4d6a581-9b42-41dc-9a4a-278fe5d6591c;
  style f4d6a581-9b42-41dc-9a4a-278fe5d6591c stroke:#2c3143,stroke-width:4px;
  11["Transpose matrix"];
  10 -->|output| 11;
  e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5["Output\nfiltered matrix (by cells) transposed"];
  11 --> e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5;
  style e4eb8fb3-2028-41fb-8aca-b1c0a6e6bfe5 stroke:#2c3143,stroke-width:4px;
  12["Filter matrix by genes"];
  8 -->|out_file1| 12;
  11 -->|out_file| 12;
  c0481255-0187-407c-9f29-f4c0069d9285["Output\nPre-filtered matrix (by cells & genes)"];
  12 --> c0481255-0187-407c-9f29-f4c0069d9285;
  style c0481255-0187-407c-9f29-f4c0069d9285 stroke:#2c3143,stroke-width:4px;
  13["Remove duplicate column genes IDs"];
  12 -->|out_file1| 13;
  4dcd8e60-1298-4886-be8f-af1eac9f20f7["Output\nFiltered matrix (by cells & genes)"];
  13 --> 4dcd8e60-1298-4886-be8f-af1eac9f20f7;
  style 4dcd8e60-1298-4886-be8f-af1eac9f20f7 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

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• 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”
• 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/scrna-case_monocle3-trajectories/workflows/Galaxy-Workflow-AnnData_object_to_Monocle_input_files.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