AnnData object to Monocle input files
single-cell-scrna-case_monocle3-trajectories/galaxy-workflow-anndata-object-to-monocle-input-files
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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
Input | Label |
---|---|
Input dataset | AnnData to extract genes & cells annotations |
Input dataset | AnnData before processing to extract clean expression matrix |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | Extract cell annotations |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | Extract gene annotations |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | Extract clean expression matrix |
Filter1 | Filter | Filter out unwanted cell types |
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.2 | Column Regex Find And Replace | gene_short_name annotation |
Cut1 | Cut | Cut cells IDs |
Cut1 | Cut | Cut genes IDs |
join1 | Join two Datasets | Filter matrix (by cells) |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 | Advanced Cut | Remove duplicate column (cells IDs) |
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2 | Transpose | Transpose matrix |
join1 | Join two Datasets | Filter matrix (by genes) |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 | Advanced Cut | Remove duplicate column (genes IDs) |
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
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
1 | 327fd2b84 | 2022-11-12 17:14:25 | Making a single cell topics |
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