Ecoli Comparison

assembly-ecoli_comparison/ecoli-comparison

Author(s)

version Version
3
last_modification Last updated
Jan 23, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
assembly

Features

Tutorial
hands_on Making sense of a newly assembled genome

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00006
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Collapse Collection"];
  6 -->|output| 10;
  11["Text transformation"];
  7 -->|output| 11;
  12["Add column"];
  8 -->|out_file1| 12;
  13["LASTZ"];
  9 -->|output| 13;
  3 -->|output| 13;
  14["random_lines1"];
  10 -->|output| 14;
  15["Filter"];
  10 -->|output| 15;
  16["Search in textfiles"];
  11 -->|output| 16;
  17["Concatenate datasets"];
  11 -->|output| 17;
  9 -->|output| 17;
  18["Cut"];
  12 -->|out_file1| 18;
  19["Text transformation"];
  13 -->|output| 19;
  2["ℹ️ Input Collection\nInput dataset collection"];
  style 2 stroke:#2c3143,stroke-width:4px;
  20["Datamash"];
  15 -->|out_file1| 20;
  21["Compute sequence length"];
  17 -->|out_file1| 21;
  22["Collapse Collection"];
  18 -->|out_file1| 22;
  23["Merge Columns"];
  19 -->|output| 23;
  24["Select"];
  20 -->|out_file| 24;
  25["Sort"];
  21 -->|output| 25;
  26["Collapse Collection"];
  23 -->|out_file1| 26;
  27["Cut"];
  26 -->|output| 27;
  28["Cut"];
  26 -->|output| 28;
  29["Concatenate datasets"];
  27 -->|out_file1| 29;
  28 -->|out_file1| 29;
  3["ℹ️ Input Collection\nInput dataset collection"];
  style 3 stroke:#2c3143,stroke-width:4px;
  30["SortBED"];
  29 -->|out_file1| 30;
  31["ComplementBed"];
  25 -->|outfile| 31;
  30 -->|output| 31;
  32["Filter"];
  31 -->|output| 32;
  33["Filter"];
  32 -->|out_file1| 33;
  34["Intersect intervals"];
  33 -->|out_file1| 34;
  22 -->|output| 34;
  35["Join two Datasets"];
  34 -->|output| 35;
  1 -->|output| 35;
  4["ℹ️ Input Collection\nInput dataset collection"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Filter sequences by length"];
  0 -->|output| 5;
  6["LASTZ"];
  2 -->|output| 6;
  0 -->|output| 6;
  7["Collapse Collection"];
  3 -->|output| 7;
  8["Select"];
  4 -->|output| 8;
  9["Text transformation"];
  5 -->|output| 9;

Inputs

Input Label
Input dataset
Input dataset
Input dataset collection
Input dataset collection
Input dataset collection

Outputs

From Output Label

Tools

Tool Links
Cut1
Filter1
Grep1
cat1
join1
random_lines1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
6 48cf52ea8 2020-01-23 09:45:24 on purpose mistake fixed
5 b3f798014 2020-01-22 17:38:04 test
4 230f6e12f 2020-01-22 15:10:52 linting fix
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 485411d09 2019-01-08 15:58:59 workflow for ecoli_comparison

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/ecoli_comparison/workflows/ecoli-comparison.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