pox-virus-tiled-amplicon-ref-masking

variant-analysis-pox-tiled-amplicon/pox-virus-tiled-amplicon-ref-masking

Author(s)
Viktoria Isabel Schwarz, Wolfgang Maier
Version
2
Last updated
May 22, 2023
License
MIT
Tags
GTN
variant-analysis

Features
Tutorial
Pox virus genome analysis from tiled-amplicon sequencing data
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00265
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nPrimer Scheme"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nReference FASTA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Select pool1 primers"];
  0 -->|output| 2;
  3["Select pool2 primers"];
  0 -->|output| 3;
  4["Compute sequence length"];
  1 -->|output| 4;
  5["Datamash"];
  2 -->|out_file1| 5;
  6["Datamash"];
  3 -->|out_file1| 6;
  7["Cut"];
  4 -->|output| 7;
  8["Compute"];
  5 -->|out_file| 8;
  9["Get start position of Pool2"];
  6 -->|out_file| 9;
  10["Get end position of sequence"];
  7 -->|out_file1| 10;
  11["Get end position of Pool1"];
  8 -->|out_file1| 11;
  12["Compose text parameter value"];
  9 -->|text_param| 12;
  13["Compose text parameter value"];
  11 -->|text_param| 13;
  10 -->|text_param| 13;
  14["Mask Reference for Pool2"];
  1 -->|output| 14;
  12 -->|out1| 14;
  af755a5e-2b20-49bc-9d52-34781f937f48["Output\nmasked_ref_pool2"];
  14 --> af755a5e-2b20-49bc-9d52-34781f937f48;
  style af755a5e-2b20-49bc-9d52-34781f937f48 stroke:#2c3143,stroke-width:4px;
  15["Mask Reference for Pool1"];
  1 -->|output| 15;
  13 -->|out1| 15;
  0c3b5b20-c426-428c-a08b-c835a82477c1["Output\nmasked_ref_pool1"];
  15 --> 0c3b5b20-c426-428c-a08b-c835a82477c1;
  style 0c3b5b20-c426-428c-a08b-c835a82477c1 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Primer Scheme
Input dataset Reference FASTA

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0 maskseq Mask Reference for Pool2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0 maskseq Mask Reference for Pool1

Tools

Tool Links
Cut1
Grep1
param_value_from_file
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2 View in ToolShed

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

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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
2 79db81a7c 2023-05-22 07:23:03 Update pox-virus-tiled-amplicon-ref-masking.ga
1 314d08f56 2023-04-23 22:36:03 Add some material for new pox virus tiled amplicon tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/pox-tiled-amplicon/workflows/pox-virus-tiled-amplicon-ref-masking.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