Workflows

These workflows are associated with Converting NCBI Data to the AnnData Format

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.

NCBI to Anndata
Morgan Howells, Pavankumar Videm

Last updated Dec 13, 2023

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Australia Galaxy Main Galaxy Europe Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nGSM5353219_PA_PB1B_Pool_2_S24_L001_dge.txt"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGSM5353223_PA_PB2B_Pool_2_S26_L001_dge.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGSM5353218_PA_PB1B_Pool_1_2_S74_L003_dge.txt"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nGSM5353216_PA_PB1A_Pool_1_3_S50_L002_dge.txt"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nGSM5353221_PA_PB2A_Pool_1_3_S25_L001_dge.txt"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nGSM5353215_PA_AUG_PB_1B_S2_dge.txt"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nGSM5353222_PA_PB2B_Pool_1_3_S52_L002_dge.txt"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\nGSM5353220_PA_PB1B_Pool_3_S51_L002_dge.txt"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nGSM5353217_PA_PB1A_Pool_2_S107_L004_dge.txt"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nGSM5353214_PA_AUG_PB_1A_S1_dge.txt"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["Import Anndata and loom"];
  0 -->|output| 10;
  11["Import Anndata and loom"];
  1 -->|output| 11;
  12["Import Anndata and loom"];
  2 -->|output| 12;
  13["Import Anndata and loom"];
  3 -->|output| 13;
  14["Import Anndata and loom"];
  4 -->|output| 14;
  15["Import Anndata and loom"];
  5 -->|output| 15;
  16["Import Anndata and loom"];
  6 -->|output| 16;
  17["Import Anndata and loom"];
  7 -->|output| 17;
  18["Import Anndata and loom"];
  8 -->|output| 18;
  19["Import Anndata and loom"];
  9 -->|output| 19;
  20["Manipulate AnnData"];
  10 -->|anndata| 20;
  21["Manipulate AnnData"];
  11 -->|anndata| 21;
  22["Manipulate AnnData"];
  12 -->|anndata| 22;
  23["Manipulate AnnData"];
  13 -->|anndata| 23;
  24["Manipulate AnnData"];
  14 -->|anndata| 24;
  25["Manipulate AnnData"];
  15 -->|anndata| 25;
  26["Manipulate AnnData"];
  16 -->|anndata| 26;
  27["Manipulate AnnData"];
  17 -->|anndata| 27;
  28["Manipulate AnnData"];
  18 -->|anndata| 28;
  29["Manipulate AnnData"];
  19 -->|anndata| 29;
  30["Manipulate AnnData"];
  29 -->|anndata| 30;
  23 -->|anndata| 30;
  24 -->|anndata| 30;
  21 -->|anndata| 30;
  25 -->|anndata| 30;
  22 -->|anndata| 30;
  27 -->|anndata| 30;
  28 -->|anndata| 30;
  26 -->|anndata| 30;
  20 -->|anndata| 30;
  31["Inspect AnnData"];
  30 -->|anndata| 31;
  32["Replace Text"];
  31 -->|obs| 32;
  33["Replace Text"];
  31 -->|obs| 33;
  34["Replace Text"];
  31 -->|obs| 34;
  35["Replace Text"];
  31 -->|obs| 35;
  36["Cut"];
  32 -->|outfile| 36;
  37["Cut"];
  33 -->|outfile| 37;
  38["Cut"];
  34 -->|outfile| 38;
  39["Cut"];
  35 -->|outfile| 39;
  40["Paste"];
  37 -->|out_file1| 40;
  36 -->|out_file1| 40;
  41["Paste"];
  40 -->|out_file1| 41;
  38 -->|out_file1| 41;
  42["Paste"];
  41 -->|out_file1| 42;
  39 -->|out_file1| 42;
  43["Manipulate AnnData"];
  30 -->|anndata| 43;
  42 -->|out_file1| 43;
  44["Scanpy FilterCells"];
  43 -->|anndata| 44;
  45["AnnData Operations"];
  44 -->|output_h5ad| 45;
  98fdc079-8b71-4841-a9aa-a3adda888616["Output\noutput_h5ad"];
  45 --> 98fdc079-8b71-4841-a9aa-a3adda888616;
  style 98fdc079-8b71-4841-a9aa-a3adda888616 stroke:#2c3143,stroke-width:4px;
  46["Inspect AnnData"];
  45 -->|output_h5ad| 46;
  e4df8425-3c1e-439c-abe5-42b705eed1b3["Output\nobs"];
  46 --> e4df8425-3c1e-439c-abe5-42b705eed1b3;
  style e4df8425-3c1e-439c-abe5-42b705eed1b3 stroke:#2c3143,stroke-width:4px;

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 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