Query a metaplasmidome database to identify and annotate plasmids in metagenomes

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nMetaplasmidome sequences"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRaw metagenomics data"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nMetaplasmidome predicted CDS"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nKEGG Ortogolog"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nPFAM"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Map with minimap2"];
  1 -->|output| 5;
  0 -->|output| 5;
  6["Convert FASTA to Tabular"];
  1 -->|output| 6;
  7["Count GFF Features"];
  2 -->|output| 7;
  8["Cut"];
  5 -->|alignment_output| 8;
  9["Cut"];
  5 -->|alignment_output| 9;
  10["Compute"];
  8 -->|out_file1| 10;
  11["Histogram with ggplot2"];
  9 -->|out_file1| 11;
  12["Cut"];
  10 -->|out_file1| 12;
  13["Histogram"];
  10 -->|out_file1| 13;
  14["Filter"];
  10 -->|out_file1| 14;
  15["Histogram with ggplot2"];
  12 -->|out_file1| 15;
  16["Filter"];
  14 -->|out_file1| 16;
  17["Cut"];
  14 -->|out_file1| 17;
  18["Cut"];
  16 -->|out_file1| 18;
  19["Histogram with ggplot2"];
  17 -->|out_file1| 19;
  20["Join two Datasets"];
  18 -->|out_file1| 20;
  6 -->|output| 20;
  21["Cut"];
  20 -->|out_file1| 21;
  22["Cut"];
  20 -->|out_file1| 22;
  23["Add Header"];
  21 -->|out_file1| 23;
  a183cd1f-a2f6-459c-a1f7-49ac50ab0df3["Output\nMetagenomes identified as plasmids"];
  23 --> a183cd1f-a2f6-459c-a1f7-49ac50ab0df3;
  style a183cd1f-a2f6-459c-a1f7-49ac50ab0df3 stroke:#2c3143,stroke-width:4px;
  24["Sort"];
  22 -->|out_file1| 24;
  25["Join two Datasets"];
  2 -->|output| 25;
  23 -->|Data Table| 25;
  26["Unique"];
  24 -->|out_file1| 26;
  27["Cut"];
  25 -->|out_file1| 27;
  28["Tabular-to-FASTA"];
  26 -->|outfile| 28;
  7c9e9f30-c340-4738-9f3b-66cbe5bde2c3["Output\nMetagenome sequences identified as plasmids"];
  28 --> 7c9e9f30-c340-4738-9f3b-66cbe5bde2c3;
  style 7c9e9f30-c340-4738-9f3b-66cbe5bde2c3 stroke:#2c3143,stroke-width:4px;
  29["Group"];
  27 -->|out_file1| 29;
  30["Filter"];
  27 -->|out_file1| 30;
  31["Cut"];
  30 -->|out_file1| 31;
  32["Filter by keywords and/or numerical value"];
  31 -->|out_file1| 32;
  33["Replace Text"];
  32 -->|kept_lines| 33;
  34["Replace Text"];
  32 -->|discarded_lines| 34;
  35["Add Header"];
  33 -->|outfile| 35;
  36["Concatenate datasets"];
  35 -->|Data Table| 36;
  34 -->|outfile| 36;
  dd7ee5f7-b8a4-45a7-9525-8ae626364e20["Output\nCDS in metagenomes identified as plasmids"];
  36 --> dd7ee5f7-b8a4-45a7-9525-8ae626364e20;
  style dd7ee5f7-b8a4-45a7-9525-8ae626364e20 stroke:#2c3143,stroke-width:4px;
  37["Join two Datasets"];
  36 -->|out_file1| 37;
  3 -->|output| 37;
  38["Cut"];
  37 -->|out_file1| 38;
  39["Join two Datasets"];
  38 -->|out_file1| 39;
  4 -->|output| 39;
  40["Cut"];
  39 -->|out_file1| 40;
  41["Select last"];
  40 -->|out_file1| 41;
  42["Add Header"];
  41 -->|outfile| 42;
  8d4adc03-cab4-444a-8122-b891f3eca2be["Output\nCDS in metagenomes identified as plasmids + KO + PFAM"];
  42 --> 8d4adc03-cab4-444a-8122-b891f3eca2be;
  style 8d4adc03-cab4-444a-8122-b891f3eca2be stroke:#2c3143,stroke-width:4px;
  43["Filter"];
  42 -->|Data Table| 43;
  44["Filter"];
  42 -->|Data Table| 44;
  45["Group"];
  42 -->|Data Table| 45;
  46["Group"];
  43 -->|out_file1| 46;
  47["Group"];
  44 -->|out_file1| 47;
  48["Select last"];
  45 -->|out_file1| 48;
  49["Sort"];
  46 -->|out_file1| 49;
  50["Sort"];
  47 -->|out_file1| 50;
  51["Add Header"];
  48 -->|outfile| 51;
  39e36bb3-4f8d-46e1-8d26-24619c7ad36d["Output\nCDS annotation overview per metagenomic sequences"];
  51 --> 39e36bb3-4f8d-46e1-8d26-24619c7ad36d;
  style 39e36bb3-4f8d-46e1-8d26-24619c7ad36d stroke:#2c3143,stroke-width:4px;

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/metaplasmidome_query/workflows/metaplasmidome.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