MAPseq to ampvis2

microbiome-mgnify-amplicon/mapseq-to-ampvis2

Author(s)
Rand Zoabi, Mara Besemer
Version
1
Last updated
Jul 30, 2025
License
MIT
Tags
microbiome

Features
Tutorial
MGnify v5.0 Amplicon Pipeline
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Collection\nMAPseq OTU tables"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nOTU table metadata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Query Tabular"];
  0 -->|output| 2;
  3["Text reformatting"];
  0 -->|output| 3;
  4["Text reformatting"];
  2 -->|output| 4;
  5["Collapse Collection"];
  3 -->|outfile| 5;
  6["Column join"];
  4 -->|outfile| 6;
  7["Text reformatting"];
  5 -->|output| 7;
  8["Text reformatting"];
  6 -->|tabular_output| 8;
  5ffe64d6-0b41-47f3-b408-a72cfe5251fa["Output\nOTU table"];
  8 --> 5ffe64d6-0b41-47f3-b408-a72cfe5251fa;
  style 5ffe64d6-0b41-47f3-b408-a72cfe5251fa stroke:#2c3143,stroke-width:4px;
  9["Query Tabular"];
  7 -->|outfile| 9;
  804604a6-e6d7-4e47-b7aa-68c856ba70d6["Output\nTaxonomy table"];
  9 --> 804604a6-e6d7-4e47-b7aa-68c856ba70d6;
  style 804604a6-e6d7-4e47-b7aa-68c856ba70d6 stroke:#2c3143,stroke-width:4px;
  10["ampvis2 load"];
  1 -->|output| 10;
  8 -->|outfile| 10;
  9 -->|output| 10;
  912ae38e-fedf-48db-8675-5bd59a542747["Output\nAmpvis2 object"];
  10 --> 912ae38e-fedf-48db-8675-5bd59a542747;
  style 912ae38e-fedf-48db-8675-5bd59a542747 stroke:#2c3143,stroke-width:4px;
  a38b9990-2773-4f81-8753-0d0926cde18d["Output\nAmpvis2 metadata table"];
  10 --> a38b9990-2773-4f81-8753-0d0926cde18d;
  style a38b9990-2773-4f81-8753-0d0926cde18d stroke:#2c3143,stroke-width:4px;
  6d547253-9859-456a-a73d-3b19e7956b87["Output\nAmpvis2 taxonomy table"];
  10 --> 6d547253-9859-456a-a73d-3b19e7956b87;
  style 6d547253-9859-456a-a73d-3b19e7956b87 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset collection MAPseq OTU tables
Input dataset OTU table metadata

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 Text reformatting
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 Query Tabular
toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0 ampvis2 load

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ampvis2_load/ampvis2_load/2.8.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 View in ToolShed

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
  1. Click on 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 d60813869 2025-07-30 14:26:42 add topic tag
1 0125a7f84 2025-07-30 12:59:47 remove version from folder name for future-proofness

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mgnify-amplicon/workflows/mapseq-to-ampvis2.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