Workflow 3: Functional Information (quick)

microbiome-metatranscriptomics-short/workflow3-functional-information-quick

Author(s)
Bérénice Batut, Pratik Jagtap, Subina Mehta, Ray Sajulga, Emma Leith, Praveen Kumar, Saskia Hiltemann, Paul Zierep
Version
1
Last updated
Jan 15, 2024
License
MIT
Tags
asaim
metagenomics

Features
Tutorial
Metatranscriptomics analysis using microbiome RNA-seq data (short)
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00131
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nPredicted taxon relative abundances"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGene Family abundance"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPathway abundance"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Cut"];
  0 -->|output| 3;
  4["Renormalize"];
  1 -->|output| 4;
  5["Regroup"];
  1 -->|output| 5;
  6["Renormalize"];
  2 -->|output| 6;
  7["Replace"];
  4 -->|output| 7;
  8["Rename features"];
  5 -->|output| 8;
  9["Split a HUMAnN table"];
  5 -->|output| 9;
  7aba96f3-1648-4126-8e58-ca10cbd2e46d["Output\nSplit a HUMAnN table on input dataset(s): Stratified table"];
  9 --> 7aba96f3-1648-4126-8e58-ca10cbd2e46d;
  style 7aba96f3-1648-4126-8e58-ca10cbd2e46d stroke:#2c3143,stroke-width:4px;
  2c36dc33-5981-4b2c-b615-a1677002e007["Output\nSplit a HUMAnN table on input dataset(s): Unstratified table"];
  9 --> 2c36dc33-5981-4b2c-b615-a1677002e007;
  style 2c36dc33-5981-4b2c-b615-a1677002e007 stroke:#2c3143,stroke-width:4px;
  10["Unpack pathway abundances"];
  4 -->|output| 10;
  6 -->|output| 10;
  11["Combination of taxonomic and metabolic assignations for gene families"];
  7 -->|outfile| 11;
  3 -->|out_file1| 11;
  46161015-b2db-4241-846e-27dd803b0fb3["Output\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances"];
  11 --> 46161015-b2db-4241-846e-27dd803b0fb3;
  style 46161015-b2db-4241-846e-27dd803b0fb3 stroke:#2c3143,stroke-width:4px;
  12["Select"];
  8 -->|output| 12;
  13["Select"];
  8 -->|output| 13;
  14["Select"];
  8 -->|output| 14;

Inputs

Input Label
Input dataset Predicted taxon relative abundances
Input dataset Gene Family abundance
Input dataset Pathway abundance

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.7+galaxy0 Renormalize
toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.7+galaxy0 Regroup
toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.7+galaxy0 Renormalize
toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.7+galaxy0 Rename features
toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.7+galaxy0 Split a HUMAnN table
toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.7+galaxy0 Unpack pathway abundances
toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0 Combine MetaPhlAn2 and HUMAnN2 outputs Combination of taxonomic and metabolic assignations for gene families
Grep1 Select
Grep1 Select
Grep1 Select

Tools

Tool Links
Cut1
Grep1
toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.7+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.7+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.7+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.7+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.7+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 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/workflow3_functional_information_quick.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