Workflow 3: Functional Information (quick)
microbiome-metatranscriptomics-short/workflow3-functional-information-quick
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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
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/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