Workflows

These workflows are associated with Comparative gene analysis in unannotated genomes

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.

Comparative gene analysis

Anton Nekrutenko

Last updated Sep 23, 2022

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["Input dataset"];
  1["Input dataset collection"];
  2["Input dataset collection"];
  3["Diamond"];
  4["Column Regex Find And Replace"];
  5["Diamond view"];
  6["Cut"];
  7["Join two Datasets"];
  8["Cut"];
  9["Collapse Collection"];
  10["Intersect"];
  11["Filter"];
  12["Collapse Collection"];
  13["Cut"];
  14["Compute"];
  15["Compute"];
  16["Split file"];
  17["Cut"];
  18["Tabular-to-FASTA"];
  19["Cut"];
  20["MAFFT"];
  21["Filter"];
  22["Filter"];
  23["Join neighbors"];
  24["Compute"];
  25["Compute"];
  26["Concatenate datasets"];
  27["Compute"];
  28["Cut"];
  29["Compute"];
  30["Join two Datasets"];
  31["Cut"];
  0 -->|output| 3;
  1 -->|output| 3;
  2 -->|output| 4;
  3 -->|daa_output| 5;
  4 -->|out_file1| 6;
  6 -->|out_file1| 7;
  5 -->|blast_tabular| 7;
  7 -->|out_file1| 8;
  7 -->|out_file1| 9;
  6 -->|out_file1| 10;
  8 -->|out_file1| 10;
  9 -->|output| 11;
  10 -->|output| 12;
  11 -->|out_file1| 13;
  12 -->|output| 14;
  13 -->|out_file1| 15;
  15 -->|out_file1| 16;
  15 -->|out_file1| 17;
  16 -->|split_output| 18;
  17 -->|out_file1| 19;
  18 -->|output| 20;
  19 -->|out_file1| 21;
  19 -->|out_file1| 22;
  20 -->|outputAlignment| 23;
  21 -->|out_file1| 24;
  22 -->|out_file1| 25;
  24 -->|out_file1| 26;
  25 -->|out_file1| 26;
  26 -->|out_file1| 27;
  27 -->|out_file1| 28;
  28 -->|out_file1| 29;
  14 -->|out_file1| 30;
  29 -->|out_file1| 30;
  30 -->|out_file1| 31;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!

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: