Argo-Glider Nitrate QCV

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput Argo or gliders netcdf collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ninput ref dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["QCV harmonizer"];
  0 -->|output| 2;
  59be8a32-81c8-4d7f-9d6b-1925496e2ba4["Output\nHarmonized netcdf"];
  2 --> 59be8a32-81c8-4d7f-9d6b-1925496e2ba4;
  style 59be8a32-81c8-4d7f-9d6b-1925496e2ba4 stroke:#2c3143,stroke-width:4px;
  3["QCV harmonizer"];
  1 -->|output| 3;
  b653f5ff-c959-4bfc-b1fa-4b14e15a26e3["Output\nHarmonized netcd"];
  3 --> b653f5ff-c959-4bfc-b1fa-4b14e15a26e3;
  style b653f5ff-c959-4bfc-b1fa-4b14e15a26e3 stroke:#2c3143,stroke-width:4px;
  4["ODV collection manager"];
  2 -->|output_net| 4;
  6f41d5e9-67a4-4df3-a43d-f2f14201e9b2["Output\nOutput odv collection"];
  4 --> 6f41d5e9-67a4-4df3-a43d-f2f14201e9b2;
  style 6f41d5e9-67a4-4df3-a43d-f2f14201e9b2 stroke:#2c3143,stroke-width:4px;
  4506c207-81c5-48b3-8f3b-6196d2a7a8fa["Output\nCollection of files"];
  4 --> 4506c207-81c5-48b3-8f3b-6196d2a7a8fa;
  style 4506c207-81c5-48b3-8f3b-6196d2a7a8fa stroke:#2c3143,stroke-width:4px;
  5["ODV"];
  4 -->|output| 5;
  4 -->|files| 5;
  17ecda27-a1ec-4eb9-982f-2c2d7e78b09c["Output\nODV history extracted (txt)"];
  5 --> 17ecda27-a1ec-4eb9-982f-2c2d7e78b09c;
  style 17ecda27-a1ec-4eb9-982f-2c2d7e78b09c stroke:#2c3143,stroke-width:4px;
  4dafb327-cce1-4791-9c5a-d9e81d0eedc5["Output\noutputs_all"];
  5 --> 4dafb327-cce1-4791-9c5a-d9e81d0eedc5;
  style 4dafb327-cce1-4791-9c5a-d9e81d0eedc5 stroke:#2c3143,stroke-width:4px;
  6["ODV history manager"];
  5 -->|outputs_txt| 6;
  4 -->|output| 6;
  2 -->|output_net| 6;
  8caa3fb4-a850-470d-8f1e-896a6d3e87d7["Output\ncsv_files"];
  6 --> 8caa3fb4-a850-470d-8f1e-896a6d3e87d7;
  style 8caa3fb4-a850-470d-8f1e-896a6d3e87d7 stroke:#2c3143,stroke-width:4px;
  71151e69-c3a6-40fc-b136-acbbe2a9ba02["Output\nnc_files_qced"];
  6 --> 71151e69-c3a6-40fc-b136-acbbe2a9ba02;
  style 71151e69-c3a6-40fc-b136-acbbe2a9ba02 stroke:#2c3143,stroke-width:4px;
  7["BioGeoChemical calibration"];
  6 -->|nc_files| 7;
  3 -->|output_net| 7;
  1e88137a-1f5f-4c39-a17b-0e3b3031d5f6["Output\nnc_files_calibrated"];
  7 --> 1e88137a-1f5f-4c39-a17b-0e3b3031d5f6;
  style 1e88137a-1f5f-4c39-a17b-0e3b3031d5f6 stroke:#2c3143,stroke-width:4px;
  828728e4-e0ad-42c0-aecc-50be6b9d1c55["Output\ntar_files"];
  7 --> 828728e4-e0ad-42c0-aecc-50be6b9d1c55;
  style 828728e4-e0ad-42c0-aecc-50be6b9d1c55 stroke:#2c3143,stroke-width:4px;
  3ca878b2-2fc7-4bbf-b17d-24ddcd4229e9["Output\npng_files"];
  7 --> 3ca878b2-2fc7-4bbf-b17d-24ddcd4229e9;
  style 3ca878b2-2fc7-4bbf-b17d-24ddcd4229e9 stroke:#2c3143,stroke-width:4px;
  4a002629-0a44-439d-a7df-378f44eabd05["Output\nlog_files"];
  7 --> 4a002629-0a44-439d-a7df-378f44eabd05;
  style 4a002629-0a44-439d-a7df-378f44eabd05 stroke:#2c3143,stroke-width:4px;
  8["ODV collection manager"];
  7 -->|nc_files| 8;
  a71098e6-8077-4b1b-b513-433f2842eed9["Output\nfiles"];
  8 --> a71098e6-8077-4b1b-b513-433f2842eed9;
  style a71098e6-8077-4b1b-b513-433f2842eed9 stroke:#2c3143,stroke-width:4px;
  5688582d-97f8-48e4-a922-1425e4b87a4f["Output\noutput odv collection (txt)"];
  8 --> 5688582d-97f8-48e4-a922-1425e4b87a4f;
  style 5688582d-97f8-48e4-a922-1425e4b87a4f stroke:#2c3143,stroke-width:4px;
  9["ODV"];
  8 -->|output| 9;

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/climate/tutorials/ocean_qcv_analysis/workflows/Galaxy-Workflow-Argo-Glider_Nitrate_QCV.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