End-to-end EI+ mass spectra prediction workflow using QCxMS

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nInput Molecules with SMILES and NAME without a header."];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nNumber of conformers to generate"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nOptimization Levels"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["ℹ️ Input Parameter\nQC Method"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["Cut SMILES column"];
  0 -->|output| 4;
  5["Cut NAME column"];
  0 -->|output| 5;
  6["Split file"];
  4 -->|output| 6;
  7["Split file"];
  5 -->|output| 7;
  8["Parse parameter value"];
  7 -->|list_output_tab| 8;
  9["Convert compounds from SMILES to SDF and add the name as title."];
  8 -->|text_param| 9;
  6 -->|list_output_tab| 9;
  10["Merge the individual SDF files"];
  9 -->|outfile| 10;
  11["Generate conformers"];
  10 -->|out_file1| 11;
  1 -->|output| 11;
  f4f8881e-cd64-42ae-8435-1288e4e473b5["Output\nconformer_output"];
  11 --> f4f8881e-cd64-42ae-8435-1288e4e473b5;
  style f4f8881e-cd64-42ae-8435-1288e4e473b5 stroke:#2c3143,stroke-width:4px;
  12["Molecular format conversion "];
  11 -->|outfile| 12;
  5dcb6f02-62c9-4f43-9810-a10052b59b41["Output\nXYZ output"];
  12 --> 5dcb6f02-62c9-4f43-9810-a10052b59b41;
  style 5dcb6f02-62c9-4f43-9810-a10052b59b41 stroke:#2c3143,stroke-width:4px;
  13["xTB molecular optimization"];
  12 -->|file_outputs| 13;
  2 -->|output| 13;
  01a9a1af-e225-4613-94f9-dfdad37c93a2["Output\noptimized output"];
  13 --> 01a9a1af-e225-4613-94f9-dfdad37c93a2;
  style 01a9a1af-e225-4613-94f9-dfdad37c93a2 stroke:#2c3143,stroke-width:4px;
  14["QCxMS neutral run"];
  3 -->|output| 14;
  13 -->|output| 14;
  e6e6a07b-d478-4a87-b491-42abee9094b1["Output\n[.in] output"];
  14 --> e6e6a07b-d478-4a87-b491-42abee9094b1;
  style e6e6a07b-d478-4a87-b491-42abee9094b1 stroke:#2c3143,stroke-width:4px;
  969b3e2f-fbee-48f9-829a-c0032580e6f8["Output\n[.xyz] output"];
  14 --> 969b3e2f-fbee-48f9-829a-c0032580e6f8;
  style 969b3e2f-fbee-48f9-829a-c0032580e6f8 stroke:#2c3143,stroke-width:4px;
  dc4811ad-6cff-42cc-a2f8-52ab585f47fe["Output\n[.start] output"];
  14 --> dc4811ad-6cff-42cc-a2f8-52ab585f47fe;
  style dc4811ad-6cff-42cc-a2f8-52ab585f47fe stroke:#2c3143,stroke-width:4px;
  15["QCxMS production run"];
  14 -->|coords1| 15;
  14 -->|coords2| 15;
  14 -->|coords3| 15;
  fc53168a-99f8-441c-9325-2d812bf03100["Output\nres output"];
  15 --> fc53168a-99f8-441c-9325-2d812bf03100;
  style fc53168a-99f8-441c-9325-2d812bf03100 stroke:#2c3143,stroke-width:4px;
  16["Filter failed datasets"];
  15 -->|res_files| 16;
  17["QCxMS get results"];
  12 -->|file_outputs| 17;
  16 -->|output| 17;
  d81bf92a-604c-46b9-86a9-bf3c2281ebcb["Output\nMSP output"];
  17 --> d81bf92a-604c-46b9-86a9-bf3c2281ebcb;
  style d81bf92a-604c-46b9-86a9-bf3c2281ebcb 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/metabolomics/tutorials/qcxms-predictions/workflows/End-to-end-EI+-mass-spectra-prediction-workflow-using-QCxMS.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