Workflow 3: Functional Information
microbiome-metatranscriptomics-short/workflow3-functional-information
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flowchart TD 0["ℹ️ Input Dataset\nInterlaced non-rRNA reads"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nPredicted taxon relative abundances"]; style 1 stroke:#2c3143,stroke-width:4px; 2["Cut"]; 1 -->|output| 2; 3["Metabolic assignation"]; 0 -->|output| 3; 1 -->|output| 3; 65797303-6f12-4ae8-9511-1af40f52e71d["Output\nHUMAnN on input dataset(s): Pathways and their abundance"]; 3 --> 65797303-6f12-4ae8-9511-1af40f52e71d; style 65797303-6f12-4ae8-9511-1af40f52e71d stroke:#2c3143,stroke-width:4px; 5cae6935-448b-4af9-ad78-7b17490e4d4a["Output\nHUMAnN on input dataset(s): Pathways and their coverage"]; 3 --> 5cae6935-448b-4af9-ad78-7b17490e4d4a; style 5cae6935-448b-4af9-ad78-7b17490e4d4a stroke:#2c3143,stroke-width:4px; 60492d72-7b3c-45c9-b32b-b6374ab08228["Output\nHUMAnN on input dataset(s): Log"]; 3 --> 60492d72-7b3c-45c9-b32b-b6374ab08228; style 60492d72-7b3c-45c9-b32b-b6374ab08228 stroke:#2c3143,stroke-width:4px; ba124b0f-cbd5-4b65-b87a-84cfa578a927["Output\nHUMAnN on input dataset(s): Gene families and their abundance"]; 3 --> ba124b0f-cbd5-4b65-b87a-84cfa578a927; style ba124b0f-cbd5-4b65-b87a-84cfa578a927 stroke:#2c3143,stroke-width:4px; 4["Renormalize"]; 3 -->|gene_families_tsv| 4; 5["Renormalize"]; 3 -->|pathabundance_tsv| 5; 6["Regroup"]; 3 -->|gene_families_tsv| 6; 7["Replace"]; 4 -->|output| 7; 8["Unpack pathway abundances"]; 4 -->|output| 8; 5 -->|output| 8; 9["Rename features"]; 6 -->|output| 9; 10["Split a HUMAnN table"]; 6 -->|output| 10; 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c["Output\nSplit a HUMAnN table on input dataset(s): Unstratified table"]; 10 --> 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c; style 1ff60d0a-4a64-44c0-8b6f-bbdfa8566a0c stroke:#2c3143,stroke-width:4px; 6a65ee93-3a2e-4a81-94ff-35917396bdfa["Output\nSplit a HUMAnN table on input dataset(s): Stratified table"]; 10 --> 6a65ee93-3a2e-4a81-94ff-35917396bdfa; style 6a65ee93-3a2e-4a81-94ff-35917396bdfa stroke:#2c3143,stroke-width:4px; 11["Combination of taxonomic and metabolic assignations for gene families"]; 7 -->|outfile| 11; 2 -->|out_file1| 11; b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2["Output\nCombine MetaPhlAn2 and HUMAnN2 outputs on input dataset(s): Gene family abundances related to genus/species abundances"]; 11 --> b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2; style b34cf972-ec0c-4ecc-ab77-bd0e61d8a0e2 stroke:#2c3143,stroke-width:4px; 12["Select"]; 9 -->|output| 12; 13["Select"]; 9 -->|output| 13; 14["Select"]; 9 -->|output| 14;
Inputs
Input | Label |
---|---|
Input dataset | Interlaced non-rRNA reads |
Input dataset | Predicted taxon relative abundances |
Outputs
From | Output | Label |
---|---|---|
Cut1 | Cut | |
toolshed.g2.bx.psu.edu/repos/iuc/humann/humann/3.7+galaxy0 | HUMAnN | Metabolic assignation |
toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.6.0+galaxy0 | Renormalize | |
toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.6.0+galaxy0 | Renormalize | |
toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.6.0+galaxy0 | Regroup | |
toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.6.0+galaxy0 | Unpack pathway abundances | |
toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.6.0+galaxy0 | Rename features | |
toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.6.0+galaxy0 | Split a HUMAnN table | |
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.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