Workflows

These workflows are associated with From small to large-scale genome comparison

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.

flowchart TD
  0["ℹ️ Input Dataset\nQuery chromosome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference chromosome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Chromeister"];
  1 -->|output| 2;
  0 -->|output| 2;
  58cf0c0c-9200-4ba4-9727-6d908ccdfa9a["Output\nChromeister on input dataset(s): Detected events"];
  2 --> 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a;
  style 58cf0c0c-9200-4ba4-9727-6d908ccdfa9a stroke:#2c3143,stroke-width:4px;
  2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c["Output\nChromeister on input dataset(s): Comparison metainformation"];
  2 --> 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c;
  style 2afd0e7c-d1cf-4bfd-bec6-6cc237ff3e2c stroke:#2c3143,stroke-width:4px;
  c248576c-1c39-416c-99d0-40c520e3da67["Output\nChromeister on input dataset(s): Comparison dotplot"];
  2 --> c248576c-1c39-416c-99d0-40c520e3da67;
  style c248576c-1c39-416c-99d0-40c520e3da67 stroke:#2c3143,stroke-width:4px;
  5f9aad77-f9ee-4932-ab22-bb5fd83f416c["Output\nChromeister on input dataset(s): Comparison matrix"];
  2 --> 5f9aad77-f9ee-4932-ab22-bb5fd83f416c;
  style 5f9aad77-f9ee-4932-ab22-bb5fd83f416c stroke:#2c3143,stroke-width:4px;
  dea450c2-7126-43dc-af7a-9f2b704c76dd["Output\nChromeister on input dataset(s): Comparison score"];
  2 --> dea450c2-7126-43dc-af7a-9f2b704c76dd;
  style dea450c2-7126-43dc-af7a-9f2b704c76dd stroke:#2c3143,stroke-width:4px;
  9a03f722-5588-4a3f-b70e-0ec9979c16dd["Output\nChromeister on input dataset(s): Detected events plot"];
  2 --> 9a03f722-5588-4a3f-b70e-0ec9979c16dd;
  style 9a03f722-5588-4a3f-b70e-0ec9979c16dd stroke:#2c3143,stroke-width:4px;
	

flowchart TD
  0["ℹ️ Input Dataset\nQuery sequence"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference sequence"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Gecko"];
  1 -->|output| 2;
  0 -->|output| 2;
  6275abc1-d74e-45a7-b8ab-3c88426cc488["Output\nGecko on input dataset(s): CSV"];
  2 --> 6275abc1-d74e-45a7-b8ab-3c88426cc488;
  style 6275abc1-d74e-45a7-b8ab-3c88426cc488 stroke:#2c3143,stroke-width:4px;
  3["Text reformatting"];
  2 -->|alignments2| 3;
  4["ClustalW"];
  3 -->|outfile| 4;
  d63c1172-a591-4bf6-b307-052ca19e7098["Output\nClustalW on input dataset(s): clustal"];
  4 --> d63c1172-a591-4bf6-b307-052ca19e7098;
  style d63c1172-a591-4bf6-b307-052ca19e7098 stroke:#2c3143,stroke-width:4px;
  d7758e3a-522d-4439-8c9a-03f784284ebd["Output\nClustalW on input dataset(s): dnd"];
  4 --> d7758e3a-522d-4439-8c9a-03f784284ebd;
  style d7758e3a-522d-4439-8c9a-03f784284ebd stroke:#2c3143,stroke-width:4px;
	

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: