Workflow 2: Community Profile

microbiome-metatranscriptomics-short/workflow2-community-profile

Author(s)
Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep
version Version
1
last_modification Last updated
Jan 15, 2024
license License
MIT
galaxy-tags Tags

Features

Tutorial
hands_on Metatranscriptomics analysis using microbiome RNA-seq data (short)
workflow Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00129
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nQC controlled forward reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nQC controlled reverse reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Taxonomic assignation"];
  0 -->|output| 2;
  1 -->|output| 2;
  b3e3198d-394e-4aeb-ba6c-9e73bfe8d049["Output\nMetaPhlAn on input dataset(s): SAM file"];
  2 --> b3e3198d-394e-4aeb-ba6c-9e73bfe8d049;
  style b3e3198d-394e-4aeb-ba6c-9e73bfe8d049 stroke:#2c3143,stroke-width:4px;
  a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b["Output\nMetaPhlAn on input dataset(s): Predicted taxon relative abundances"];
  2 --> a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b;
  style a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b stroke:#2c3143,stroke-width:4px;
  30a9e692-8d31-45bd-9246-81ddead3ba03["Output\nMetaPhlAn on input dataset(s): Bowtie2 output"];
  2 --> 30a9e692-8d31-45bd-9246-81ddead3ba03;
  style 30a9e692-8d31-45bd-9246-81ddead3ba03 stroke:#2c3143,stroke-width:4px;
  2465a9ab-a28e-4c58-b647-b6792f77ddf2["Output\nMetaPhlAn on input dataset(s): BIOM file"];
  2 --> 2465a9ab-a28e-4c58-b647-b6792f77ddf2;
  style 2465a9ab-a28e-4c58-b647-b6792f77ddf2 stroke:#2c3143,stroke-width:4px;
  3["Cut"];
  2 -->|output_file| 3;
  4["Krona pie chart"];
  2 -->|krona_output_file| 4;
  5["Export to GraPhlAn"];
  3 -->|out_file1| 5;
  f578de2e-6edd-4ee0-9bc4-9371d6fd957f["Output\nExport to GraPhlAn on input dataset(s): Annotation"];
  5 --> f578de2e-6edd-4ee0-9bc4-9371d6fd957f;
  style f578de2e-6edd-4ee0-9bc4-9371d6fd957f stroke:#2c3143,stroke-width:4px;
  4e9cfae0-ee7b-4347-84db-5a3e24688e50["Output\nExport to GraPhlAn on input dataset(s): Tree"];
  5 --> 4e9cfae0-ee7b-4347-84db-5a3e24688e50;
  style 4e9cfae0-ee7b-4347-84db-5a3e24688e50 stroke:#2c3143,stroke-width:4px;
  6["Generation, personalization and annotation of tree"];
  5 -->|annotation| 6;
  5 -->|tree| 6;
  edf4ecaf-dddd-43a3-ba4a-d683671c1815["Output\nGeneration, personalization and annotation of tree on input dataset(s): Tree in PhyloXML"];
  6 --> edf4ecaf-dddd-43a3-ba4a-d683671c1815;
  style edf4ecaf-dddd-43a3-ba4a-d683671c1815 stroke:#2c3143,stroke-width:4px;
  7["Visualisation GraPhlAn"];
  6 -->|output_tree| 7;
  b304fe87-de7e-48d2-8774-9c52d2395fa4["Output\nGraPhlAn on input dataset(s): PNG"];
  7 --> b304fe87-de7e-48d2-8774-9c52d2395fa4;
  style b304fe87-de7e-48d2-8774-9c52d2395fa4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset QC controlled forward reads
Input dataset QC controlled reverse reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0 MetaPhlAn Taxonomic assignation
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 Krona pie chart
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 Export to GraPhlAn
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0 Generation, personalization and annotation of tree
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0 GraPhlAn Visualisation (GraPhlAn)

Tools

Tool Links
Cut1
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0 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
  • 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 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metatranscriptomics-short/workflows/workflow2_community_profile.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