Taxonomy Profiling and Visualization with Krona
microbiome-pathogen-detection-from-nanopore-foodborne-data/taxonomy-profiling-and-visualisation-with-krona
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flowchart TD 0["ℹ️ Input Collection\ncollection_of_preprocessed_samples"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Parameter\nkraken_database"]; style 1 fill:#ded,stroke:#393,stroke-width:4px; 2["Kraken2"]; 1 -->|output| 2; 0 -->|output| 2; 26f9041f-d8a4-4f64-8a53-404d5c7e2f61["Output\nkraken2_with_pluspf_database_output"]; 2 --> 26f9041f-d8a4-4f64-8a53-404d5c7e2f61; style 26f9041f-d8a4-4f64-8a53-404d5c7e2f61 stroke:#2c3143,stroke-width:4px; f2ddd05b-66a0-4cea-9da6-ed107eecbe1b["Output\nkraken2_with_pluspf_database_output_report"]; 2 --> f2ddd05b-66a0-4cea-9da6-ed107eecbe1b; style f2ddd05b-66a0-4cea-9da6-ed107eecbe1b stroke:#2c3143,stroke-width:4px; 3["Krakentools: Convert kraken report file"]; 2 -->|report_output| 3; c490ab8d-1b1d-4914-aa51-a62a967a4018["Output\nconverted_kraken_report"]; 3 --> c490ab8d-1b1d-4914-aa51-a62a967a4018; style c490ab8d-1b1d-4914-aa51-a62a967a4018 stroke:#2c3143,stroke-width:4px; 4["Krona pie chart"]; 3 -->|output| 4; dcc857c6-f579-4c74-84ec-bb6ce3794a56["Output\nkrona_pie_chart"]; 4 --> dcc857c6-f579-4c74-84ec-bb6ce3794a56; style dcc857c6-f579-4c74-84ec-bb6ce3794a56 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset collection | collection_of_preprocessed_samples |
Input parameter | kraken_database |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 | Kraken2 | |
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2+galaxy1 | Krakentools: Convert kraken report file | |
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 | Krona pie chart |
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 |
---|---|---|---|
2 | cdd93376a | 2024-06-06 12:00:29 | adding tags to some of the workflow outputs, updating the training with the latest PathoGFAIR workflows updates |
1 | c63ce23c7 | 2024-05-26 12:29:47 | updating workflows file names |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/taxonomy_profiling_and_visualisation_with_krona.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