GigaScience-IEDB-PepQuery-Neoantigen

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nIEDB-optityle-seq2hla-alleles"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nFASTA-for-IEDB"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nMSMS-Spectrum"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["IEDB"];
  0 -->|output| 3;
  1 -->|output| 3;
  a7fdb54c-93ed-4235-b76b-caa7c15d0dfc["Output\niedb_binding_predictions"];
  3 --> a7fdb54c-93ed-4235-b76b-caa7c15d0dfc;
  style a7fdb54c-93ed-4235-b76b-caa7c15d0dfc stroke:#2c3143,stroke-width:4px;
  4["Filter-weak-binder"];
  3 -->|output| 4;
  da34763e-d406-4366-af85-cb805e168105["Output\nWeak-Binders"];
  4 --> da34763e-d406-4366-af85-cb805e168105;
  style da34763e-d406-4366-af85-cb805e168105 stroke:#2c3143,stroke-width:4px;
  5["Filter-strong-binders"];
  3 -->|output| 5;
  0f023395-964b-42c2-9e4f-b05a929bf064["Output\nStrong-Binders"];
  5 --> 0f023395-964b-42c2-9e4f-b05a929bf064;
  style 0f023395-964b-42c2-9e4f-b05a929bf064 stroke:#2c3143,stroke-width:4px;
  6["pivot_table_iedb_results-weak"];
  4 -->|out_file1| 6;
  ec56600f-a26b-4931-8431-d73da746ca4c["Output\niedb_results_pivot_table_weak"];
  6 --> ec56600f-a26b-4931-8431-d73da746ca4c;
  style ec56600f-a26b-4931-8431-d73da746ca4c stroke:#2c3143,stroke-width:4px;
  7["pivot_table_iedb_results_strong"];
  5 -->|out_file1| 7;
  332fcd7f-7ace-4d23-9ea1-3a53a993db2b["Output\niedb_results_pivot_table_strong"];
  7 --> 332fcd7f-7ace-4d23-9ea1-3a53a993db2b;
  style 332fcd7f-7ace-4d23-9ea1-3a53a993db2b stroke:#2c3143,stroke-width:4px;
  8["Removing_first_line-weak"];
  6 -->|table| 8;
  991c6d8e-f192-4706-bd2f-a5a247d43361["Output\nheader_removed_for_filter-weak"];
  8 --> 991c6d8e-f192-4706-bd2f-a5a247d43361;
  style 991c6d8e-f192-4706-bd2f-a5a247d43361 stroke:#2c3143,stroke-width:4px;
  9["Removing_first_line-strong"];
  7 -->|table| 9;
  c8c7951d-4b89-44f7-9583-86cd69b3212b["Output\nheader removed for filter-strong"];
  9 --> c8c7951d-4b89-44f7-9583-86cd69b3212b;
  style c8c7951d-4b89-44f7-9583-86cd69b3212b stroke:#2c3143,stroke-width:4px;
  10["Peptide-Column-extraction-weak"];
  8 -->|out_file1| 10;
  45fc4362-d338-402f-903c-e22630895f7b["Output\nPeptide-for-PepQuery-weak"];
  10 --> 45fc4362-d338-402f-903c-e22630895f7b;
  style 45fc4362-d338-402f-903c-e22630895f7b stroke:#2c3143,stroke-width:4px;
  11["Peptide-Column-extraction-strong"];
  9 -->|out_file1| 11;
  caa24097-6a49-4950-8271-42ce94ac37e6["Output\nPeptide-for-PepQuery-strong"];
  11 --> caa24097-6a49-4950-8271-42ce94ac37e6;
  style caa24097-6a49-4950-8271-42ce94ac37e6 stroke:#2c3143,stroke-width:4px;
  12["PepQuery-IEDB-Peptides-weak"];
  10 -->|out_file1| 12;
  2 -->|output| 12;
  23f3a99d-81cf-4fe0-bb63-218228aec6dc["Output\nPepQuery-IEDB-Peptides-weak"];
  12 --> 23f3a99d-81cf-4fe0-bb63-218228aec6dc;
  style 23f3a99d-81cf-4fe0-bb63-218228aec6dc stroke:#2c3143,stroke-width:4px;
  a7765d0f-2282-46ce-a8e4-4aee6b3b01ce["Output\nPepQuery-IEDB-Peptides-log-weak"];
  12 --> a7765d0f-2282-46ce-a8e4-4aee6b3b01ce;
  style a7765d0f-2282-46ce-a8e4-4aee6b3b01ce stroke:#2c3143,stroke-width:4px;
  13["PepQuery-IEDB-Peptides-strong"];
  11 -->|out_file1| 13;
  2 -->|output| 13;
  854db1c7-25f2-4f0e-ba05-dd180f954f73["Output\nPepQuery-IEDB-Peptides"];
  13 --> 854db1c7-25f2-4f0e-ba05-dd180f954f73;
  style 854db1c7-25f2-4f0e-ba05-dd180f954f73 stroke:#2c3143,stroke-width:4px;
  72ad5a85-80e6-40a0-8a8a-e0e33427b984["Output\nPepQuery-IEDB-Peptides-log-strong"];
  13 --> 72ad5a85-80e6-40a0-8a8a-e0e33427b984;
  style 72ad5a85-80e6-40a0-8a8a-e0e33427b984 stroke:#2c3143,stroke-width:4px;
  14["Filtering-Confident-peptides-weak"];
  12 -->|psm_rank_txt| 14;
  cb8fceb5-ad70-459a-af65-516db31ba6d9["Output\nIEDB-Validated-NeoAntigen_Peptides-weak"];
  14 --> cb8fceb5-ad70-459a-af65-516db31ba6d9;
  style cb8fceb5-ad70-459a-af65-516db31ba6d9 stroke:#2c3143,stroke-width:4px;
  15["Filtering-Confident-peptides-strong"];
  13 -->|psm_rank_txt| 15;
  eade637d-296b-412a-bcf6-c51c72f90c6f["Output\nIEDB-Validated-NeoAntigen_Peptides-strong"];
  15 --> eade637d-296b-412a-bcf6-c51c72f90c6f;
  style eade637d-296b-412a-bcf6-c51c72f90c6f stroke:#2c3143,stroke-width:4px;
  16["Novel_NeoPeptides-weak"];
  6 -->|table| 16;
  14 -->|out_file1| 16;
  dd312a10-321b-46cf-8de6-3b17944676f3["Output\niedb_novel_peptide_x_hla_table-weak"];
  16 --> dd312a10-321b-46cf-8de6-3b17944676f3;
  style dd312a10-321b-46cf-8de6-3b17944676f3 stroke:#2c3143,stroke-width:4px;
  c5b24d01-60d3-4499-94f4-165c5985c70d["Output\niedb_predicted_neoantigens-weak"];
  16 --> c5b24d01-60d3-4499-94f4-165c5985c70d;
  style c5b24d01-60d3-4499-94f4-165c5985c70d stroke:#2c3143,stroke-width:4px;
  17["Novel_NeoPeptides-strong"];
  7 -->|table| 17;
  15 -->|out_file1| 17;
  5d9e2770-3431-421c-9f70-f9cf88dd7620["Output\niedb_novel_peptide_x_hla_table-strong"];
  17 --> 5d9e2770-3431-421c-9f70-f9cf88dd7620;
  style 5d9e2770-3431-421c-9f70-f9cf88dd7620 stroke:#2c3143,stroke-width:4px;
  c3661e5e-b0cd-4975-948e-5d5ef9e28c8a["Output\niedb_predicted_neoantigens-strong"];
  17 --> c3661e5e-b0cd-4975-948e-5d5ef9e28c8a;
  style c3661e5e-b0cd-4975-948e-5d5ef9e28c8a 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/proteomics/tutorials/neoantigen-7-hla-binding-novel-peptides/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