metaquantome-function-worklow

proteomics-metaquantome-function/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 2: Function

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00162
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: database"];
  1["metaQuantome: create samples file"];
  2["ℹ️ Input Dataset\nFunctional file"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nIntensity file"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["metaQuantome: expand"];
  0 -->|outfile| 4;
  3 -->|output| 4;
  2 -->|output| 4;
  1 -->|samples_file| 4;
  5["metaQuantome: filter"];
  4 -->|outfile| 5;
  1 -->|samples_file| 5;
  6["metaQuantome: stat"];
  5 -->|outfile| 6;
  1 -->|samples_file| 6;
  7["T2-Bar-Plot"];
  6 -->|outfile| 7;
  6 -->|outfile| 7;
  8["T4-Bar-Plot"];
  6 -->|outfile| 8;
  1 -->|samples_file| 8;
  9["T7-Bar-Plot"];
  6 -->|outfile| 9;
  1 -->|samples_file| 9;
  10["T7-T2-Volcano-Plot"];
  6 -->|outfile| 10;
  1 -->|samples_file| 10;
  11["T4-T2-Volcano-Plot"];
  6 -->|outfile| 11;
  1 -->|samples_file| 11;

Inputs

Input Label
Input dataset Functional file
Input dataset Intensity file

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0 metaQuantome: database
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0 metaQuantome: create samples file
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0 metaQuantome: expand
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0 metaQuantome: filter
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0 metaQuantome: stat
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 metaQuantome: visualize T2-Bar-Plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 metaQuantome: visualize T4-Bar-Plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 metaQuantome: visualize T7-Bar-Plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 metaQuantome: visualize T7-T2-Volcano-Plot
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 metaQuantome: visualize T4-T2-Volcano-Plot

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_viz/metaquantome_viz/2.0.2+galaxy0 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
4 9d12ea3f6 2021-11-09 16:35:24 Update main_workflow.ga
3 b44e7f7c7 2020-10-26 15:34:51 Update main_workflow.ga
2 619a94b38 2020-10-20 01:51:17 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-function/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