preparing genomic data for phylogeny recostruction (GTN)

Run Workflow in Galaxy

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• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nInput genomes as collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Replace Text"];
  0 -->|output| 1;
  6a2d3fcd-b557-4440-910d-b4c537feef20["Output\nheaders_shortened"];
  1 --> 6a2d3fcd-b557-4440-910d-b4c537feef20;
  style 6a2d3fcd-b557-4440-910d-b4c537feef20 stroke:#2c3143,stroke-width:4px;
  2["RepeatMasker"];
  1 -->|outfile| 2;
  1db6607a-343a-4a61-9a3b-43101eb8223b["Output\nrepeat_masked"];
  2 --> 1db6607a-343a-4a61-9a3b-43101eb8223b;
  style 1db6607a-343a-4a61-9a3b-43101eb8223b stroke:#2c3143,stroke-width:4px;
  3["Funannotate predict annotation"];
  2 -->|output_masked_genome| 3;
  642c1c09-82f4-4ef4-bd53-d14a583044e2["Output\nfunannotate_predicted_proteins"];
  3 --> 642c1c09-82f4-4ef4-bd53-d14a583044e2;
  style 642c1c09-82f4-4ef4-bd53-d14a583044e2 stroke:#2c3143,stroke-width:4px;
  4["Extract ORF"];
  3 -->|annot_gbk| 4;
  07fb8c04-990e-4bc7-b607-9c4161b4786d["Output\nextracted_ORFs"];
  4 --> 07fb8c04-990e-4bc7-b607-9c4161b4786d;
  style 07fb8c04-990e-4bc7-b607-9c4161b4786d stroke:#2c3143,stroke-width:4px;
  5["Regex Find And Replace"];
  4 -->|aa_output| 5;
  8dc378a8-d485-42df-8322-6cf8230257a0["Output\nsample_names_to_headers"];
  5 --> 8dc378a8-d485-42df-8322-6cf8230257a0;
  style 8dc378a8-d485-42df-8322-6cf8230257a0 stroke:#2c3143,stroke-width:4px;
  6["Collapse Collection"];
  5 -->|out_file1| 6;
  e9a55459-4a2c-4238-8494-e99ec67307ea["Output\nproteomes_to_one_file"];
  6 --> e9a55459-4a2c-4238-8494-e99ec67307ea;
  style e9a55459-4a2c-4238-8494-e99ec67307ea stroke:#2c3143,stroke-width:4px;
  7["Proteinortho"];
  5 -->|out_file1| 7;
  ee688b7a-2a9e-4480-a27a-db8cf795b635["Output\nProteinortho on input dataset(s): orthology-groups"];
  7 --> ee688b7a-2a9e-4480-a27a-db8cf795b635;
  style ee688b7a-2a9e-4480-a27a-db8cf795b635 stroke:#2c3143,stroke-width:4px;
  8["Busco"];
  5 -->|out_file1| 8;
  9["Filter"];
  7 -->|proteinortho| 9;
  10["Proteinortho grab proteins"];
  6 -->|output| 10;
  9 -->|out_file1| 10;
  8625e8b1-e3af-4afa-bf85-1a3258cbbfb2["Output\nProteinortho_extract_by_orthogroup"];
  10 --> 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2;
  style 8625e8b1-e3af-4afa-bf85-1a3258cbbfb2 stroke:#2c3143,stroke-width:4px;
  11["Regex Find And Replace"];
  10 -->|listproteinorthograbproteins| 11;
  b072d32e-f725-4833-af0b-74f4df526d9a["Output\nfasta_header_cleaned"];
  11 --> b072d32e-f725-4833-af0b-74f4df526d9a;
  style b072d32e-f725-4833-af0b-74f4df526d9a stroke:#2c3143,stroke-width:4px;
  12["ClustalW"];
  11 -->|out_file1| 12;
  f704b4b2-5214-4393-8a85-6274bda27c8c["Output\nClustalW on input dataset(s): clustal"];
  12 --> f704b4b2-5214-4393-8a85-6274bda27c8c;
  style f704b4b2-5214-4393-8a85-6274bda27c8c stroke:#2c3143,stroke-width:4px;
  13["ClipKIT. Alignment trimming software for phylogenetics."];
  12 -->|output| 13;
  37092981-191a-4413-8f60-51802dd95f9c["Output\nTrimmed alignment."];
  13 --> 37092981-191a-4413-8f60-51802dd95f9c;
  style 37092981-191a-4413-8f60-51802dd95f9c stroke:#2c3143,stroke-width:4px;
  14["PhyKit - Alignment-based functions"];
  13 -->|trimmed_output| 14;
  09ad25e3-cd68-4fb4-9c57-3e79212b8e01["Output\nConcatenated fasta alignment file"];
  14 --> 09ad25e3-cd68-4fb4-9c57-3e79212b8e01;
  style 09ad25e3-cd68-4fb4-9c57-3e79212b8e01 stroke:#2c3143,stroke-width:4px;
  1d546e4c-7e3c-499d-870c-4846feb7a46d["Output\nA partition file ready for input into RAxML or IQ-tree"];
  14 --> 1d546e4c-7e3c-499d-870c-4846feb7a46d;
  style 1d546e4c-7e3c-499d-870c-4846feb7a46d stroke:#2c3143,stroke-width:4px;
  26846814-d43a-4ce7-9f26-cfb70f184dce["Output\nAn occupancy file that summarizes the taxon occupancy per sequence"];
  14 --> 26846814-d43a-4ce7-9f26-cfb70f184dce;
  style 26846814-d43a-4ce7-9f26-cfb70f184dce 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/ecology/tutorials/phylogeny-data-prep/workflows/main_workflow.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