Molecular formula assignment and recalibration with MFAssignR package.

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nFeature table"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["MFAssignR KMDNoise"];
  0 -->|output| 1;
  2["MFAssignR HistNoise"];
  0 -->|output| 2;
  3["MFAssignR SNplot"];
  0 -->|output| 3;
  74da5be7-06ed-475c-a95a-813cc74dd124["Output\nSNplot"];
  3 --> 74da5be7-06ed-475c-a95a-813cc74dd124;
  style 74da5be7-06ed-475c-a95a-813cc74dd124 stroke:#2c3143,stroke-width:4px;
  4["MFAssignR IsoFiltR"];
  0 -->|output| 4;
  5["MFAssignR MFAssignCHO"];
  4 -->|iso_out| 5;
  4 -->|mono_out| 5;
  36722438-d25d-4107-87fa-3340ac8f55f6["Output\nplots"];
  5 --> 36722438-d25d-4107-87fa-3340ac8f55f6;
  style 36722438-d25d-4107-87fa-3340ac8f55f6 stroke:#2c3143,stroke-width:4px;
  6["MFAssignR RecalList"];
  5 -->|Unambig| 6;
  96ae5d5e-fc6d-4523-a3ad-fdc2dc9fab45["Output\nrecal_series"];
  6 --> 96ae5d5e-fc6d-4523-a3ad-fdc2dc9fab45;
  style 96ae5d5e-fc6d-4523-a3ad-fdc2dc9fab45 stroke:#2c3143,stroke-width:4px;
  7["MFAssignR FindRecalSeries"];
  6 -->|recal_series| 7;
  65060598-3645-458d-82cd-0613189020f3["Output\nfinal_series"];
  7 --> 65060598-3645-458d-82cd-0613189020f3;
  style 65060598-3645-458d-82cd-0613189020f3 stroke:#2c3143,stroke-width:4px;
  8["MFAssignR Recal"];
  5 -->|Unambig| 8;
  4 -->|iso_out| 8;
  4 -->|mono_out| 8;
  7 -->|final_series| 8;
  1f370a51-f49b-476f-ad9e-09b69a168158["Output\nMZplot"];
  8 --> 1f370a51-f49b-476f-ad9e-09b69a168158;
  style 1f370a51-f49b-476f-ad9e-09b69a168158 stroke:#2c3143,stroke-width:4px;
  9["MFAssignR MFAssign"];
  8 -->|Iso| 9;
  8 -->|Mono| 9;
  0b738f04-c31c-4949-890d-00e15b465187["Output\nNone"];
  9 --> 0b738f04-c31c-4949-890d-00e15b465187;
  style 0b738f04-c31c-4949-890d-00e15b465187 stroke:#2c3143,stroke-width:4px;
  cafc72e0-b9d0-4eb1-a8a1-9f87ea72690e["Output\nAmbig"];
  9 --> cafc72e0-b9d0-4eb1-a8a1-9f87ea72690e;
  style cafc72e0-b9d0-4eb1-a8a1-9f87ea72690e stroke:#2c3143,stroke-width:4px;
  378afd46-c896-4393-9e6c-c379609a39d1["Output\nUnambig"];
  9 --> 378afd46-c896-4393-9e6c-c379609a39d1;
  style 378afd46-c896-4393-9e6c-c379609a39d1 stroke:#2c3143,stroke-width:4px;
  7456324f-04c0-4573-8abf-fda0567b7732["Output\nplots"];
  9 --> 7456324f-04c0-4573-8abf-fda0567b7732;
  style 7456324f-04c0-4573-8abf-fda0567b7732 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

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. 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/mfassignr/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