Workflow 3: Functional Information

microbiome-metatranscriptomics-short/workflow3-functional-information

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:W00130
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\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

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/humann/3.7+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_regroup_table/humann_regroup_table/3.6.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_rename_table/humann_rename_table/3.6.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_renorm_table/humann_renorm_table/3.6.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_split_stratified_table/humann_split_stratified_table/3.6.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/humann_unpack_pathways/humann_unpack_pathways/3.6.0+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/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