MGnify amplicon summary tables

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nOTU tables"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nTaxonomic abundance summary table name"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nPhylum level taxonomic abundance summary table name"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["Query Tabular"];
  0 -->|output| 3;
  4["Text reformatting"];
  0 -->|output| 4;
  5["Text reformatting"];
  3 -->|output| 5;
  6["Group"];
  4 -->|outfile| 6;
  7["Column join"];
  5 -->|outfile| 7;
  8["Filter Tabular"];
  6 -->|out_file1| 8;
  9["Text reformatting"];
  7 -->|tabular_output| 9;
  3a506fef-a399-494c-98da-eef7f481c495["Output\nTaxonomic abundance summary table"];
  9 --> 3a506fef-a399-494c-98da-eef7f481c495;
  style 3a506fef-a399-494c-98da-eef7f481c495 stroke:#2c3143,stroke-width:4px;
  10["Text reformatting"];
  8 -->|output| 10;
  11["Column join"];
  10 -->|outfile| 11;
  12["Text reformatting"];
  11 -->|tabular_output| 12;
  59063507-c356-409b-b087-06fc1e55f7aa["Output\nphylum level taxonomic abundance summary table"];
  12 --> 59063507-c356-409b-b087-06fc1e55f7aa;
  style 59063507-c356-409b-b087-06fc1e55f7aa 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/microbiome/tutorials/mgnify-amplicon/workflows/mgnify-amplicon-summary-tables.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