metaquantome-taxonomy-workflow

proteomics-metaquantome-taxonomy/main-workflow

Author(s)

version Version
2
last_modification Last updated
Nov 11, 2021
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
proteomics

Features

Tutorial
hands_on metaQuantome 3: Taxonomy

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00163
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["metaQuantome: create samples file"];
  1["ℹ️ Input Dataset\nTaxa"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nIntensity"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["metaQuantome: database"];
  4["metaQuantome: expand"];
  3 -->|outfile| 4;
  2 -->|output| 4;
  1 -->|output| 4;
  0 -->|samples_file| 4;
  5["metaQuantome: filter"];
  4 -->|outfile| 5;
  0 -->|samples_file| 5;
  6["metaQuantome: stat"];
  5 -->|outfile| 6;
  0 -->|samples_file| 6;
  7["T2-Bar-Plot"];
  6 -->|outfile| 7;
  0 -->|samples_file| 7;
  8["T7-T2_volcano-plot"];
  6 -->|outfile| 8;
  0 -->|samples_file| 8;
  9["T4-Bar-Plot"];
  6 -->|outfile| 9;
  0 -->|samples_file| 9;
  10["T7-Bar-Plot"];
  6 -->|outfile| 10;
  0 -->|samples_file| 10;
  11["T4-T2_volcano-plot"];
  6 -->|outfile| 11;
  0 -->|samples_file| 11;

Inputs

Input Label
Input dataset Taxa
Input dataset Intensity

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0 metaQuantome: create samples file
Input dataset Taxa
Input dataset Intensity
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0 metaQuantome: database
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0 metaQuantome: expand
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0 metaQuantome: filter
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0 metaQuantome: stat
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 metaQuantome: visualize T2-Bar-Plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 metaQuantome: visualize T7-T2_volcano-plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 metaQuantome: visualize T4-Bar-Plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 metaQuantome: visualize T7-Bar-Plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 metaQuantome: visualize T4-T2_volcano-plot

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.0-0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.0-0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.0-0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.0-0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.0-0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.0-0 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
3 23fe00a8a 2021-11-09 21:53:45 Update main_workflow.ga
2 6508b4644 2020-10-20 01:55:30 Update main_workflow.ga
1 426a2746e 2020-10-16 13:04:21 tutorial skeletons generated by planemo

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-taxonomy/workflows/main_workflow.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