These workflows are associated with Taxonomic Profiling and Visualization of Metagenomic Data

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.

Taxonomic Profiling and Visualization of Metagenomic Data
Bérénice Batut

Last updated Jan 11, 2024

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Collection\nraw-reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nmetadata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Unzip collection"];
  0 -->|output| 2;
  0 -->|output| 3;
  3 --> 89301e9d-8d7e-42d6-b911-29d50ac0e8c4;
  style 89301e9d-8d7e-42d6-b911-29d50ac0e8c4 stroke:#2c3143,stroke-width:4px;
  2 -->|forward| 4;
  2 -->|reverse| 4;
  4 --> 071a64dd-2bf7-483b-a9db-989eb9177fa9;
  style 071a64dd-2bf7-483b-a9db-989eb9177fa9 stroke:#2c3143,stroke-width:4px;
  5["Krakentools: Convert kraken report file"];
  3 -->|report_output| 5;
  5 --> 3ea9e1fc-c749-4481-bd3f-592d5fcc615a;
  style 3ea9e1fc-c749-4481-bd3f-592d5fcc615a stroke:#2c3143,stroke-width:4px;
  3 -->|report_output| 6;
  1 -->|output| 6;
  3 -->|report_output| 7;
  8["Estimate Abundance at Taxonomic Level"];
  3 -->|report_output| 8;
  9["Krona pie chart"];
  4 -->|krona_output_file| 9;
  10["Krona pie chart"];
  5 -->|output| 10;
  11["Phinch Visualisation"];
  6 -->|biomOutput| 11;

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