Workflow 2: Community Profile
microbiome-metatranscriptomics-short/workflow2-community-profile
Launch in Tutorial Mode
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flowchart TD 0["ℹ️ Input Dataset\nQC controlled forward reads"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nQC controlled reverse reads"]; style 1 stroke:#2c3143,stroke-width:4px; 2["Taxonomic assignation"]; 0 -->|output| 2; 1 -->|output| 2; b3e3198d-394e-4aeb-ba6c-9e73bfe8d049["Output\nMetaPhlAn on input dataset(s): SAM file"]; 2 --> b3e3198d-394e-4aeb-ba6c-9e73bfe8d049; style b3e3198d-394e-4aeb-ba6c-9e73bfe8d049 stroke:#2c3143,stroke-width:4px; a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b["Output\nMetaPhlAn on input dataset(s): Predicted taxon relative abundances"]; 2 --> a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b; style a4ecdc94-d012-413f-a9cb-6f3e9ee70d5b stroke:#2c3143,stroke-width:4px; 30a9e692-8d31-45bd-9246-81ddead3ba03["Output\nMetaPhlAn on input dataset(s): Bowtie2 output"]; 2 --> 30a9e692-8d31-45bd-9246-81ddead3ba03; style 30a9e692-8d31-45bd-9246-81ddead3ba03 stroke:#2c3143,stroke-width:4px; 2465a9ab-a28e-4c58-b647-b6792f77ddf2["Output\nMetaPhlAn on input dataset(s): BIOM file"]; 2 --> 2465a9ab-a28e-4c58-b647-b6792f77ddf2; style 2465a9ab-a28e-4c58-b647-b6792f77ddf2 stroke:#2c3143,stroke-width:4px; 3["Cut"]; 2 -->|output_file| 3; 4["Krona pie chart"]; 2 -->|krona_output_file| 4; 5["Export to GraPhlAn"]; 3 -->|out_file1| 5; f578de2e-6edd-4ee0-9bc4-9371d6fd957f["Output\nExport to GraPhlAn on input dataset(s): Annotation"]; 5 --> f578de2e-6edd-4ee0-9bc4-9371d6fd957f; style f578de2e-6edd-4ee0-9bc4-9371d6fd957f stroke:#2c3143,stroke-width:4px; 4e9cfae0-ee7b-4347-84db-5a3e24688e50["Output\nExport to GraPhlAn on input dataset(s): Tree"]; 5 --> 4e9cfae0-ee7b-4347-84db-5a3e24688e50; style 4e9cfae0-ee7b-4347-84db-5a3e24688e50 stroke:#2c3143,stroke-width:4px; 6["Generation, personalization and annotation of tree"]; 5 -->|annotation| 6; 5 -->|tree| 6; edf4ecaf-dddd-43a3-ba4a-d683671c1815["Output\nGeneration, personalization and annotation of tree on input dataset(s): Tree in PhyloXML"]; 6 --> edf4ecaf-dddd-43a3-ba4a-d683671c1815; style edf4ecaf-dddd-43a3-ba4a-d683671c1815 stroke:#2c3143,stroke-width:4px; 7["Visualisation GraPhlAn"]; 6 -->|output_tree| 7; b304fe87-de7e-48d2-8774-9c52d2395fa4["Output\nGraPhlAn on input dataset(s): PNG"]; 7 --> b304fe87-de7e-48d2-8774-9c52d2395fa4; style b304fe87-de7e-48d2-8774-9c52d2395fa4 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | QC controlled forward reads |
Input dataset | QC controlled reverse reads |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy0 | MetaPhlAn | Taxonomic assignation |
Cut1 | Cut | |
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 | Krona pie chart | |
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.20+galaxy0 | Export to GraPhlAn | |
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0 | Generation, personalization and annotation of tree | |
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0 | GraPhlAn | Visualisation (GraPhlAn) |
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/workflow2_community_profile.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