Workflow 3: Functional Information

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy France
• Galaxy Main
• Galaxy Europe
• Import to another server (≥23.0+ only!)

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

Outputs

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

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:

Version History

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