Metaproteomics_GTN

proteomics-metaproteomics/workflow

Author(s)

version Version
7
last_modification Last updated
Feb 9, 2021
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
proteomics

Features

Tutorial
hands_on Metaproteomics tutorial

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00160
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\nSixgill generated protein FASTA File"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nDataset Collection of Bering Strait MGF Files"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGene Ontology Terms Selected"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Search GUI"];
  0 -->|output| 3;
  1 -->|output| 3;
  7516674a-b5aa-45b5-b2e8-38c1889ad2e9["Output\nSearch GUI on input dataset(s)"];
  3 --> 7516674a-b5aa-45b5-b2e8-38c1889ad2e9;
  style 7516674a-b5aa-45b5-b2e8-38c1889ad2e9 stroke:#2c3143,stroke-width:4px;
  4["Peptide Shaker"];
  3 -->|searchgui_results| 4;
  ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0["Output\nPeptide Shaker on input dataset(s): mzidentML file"];
  4 --> ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0;
  style ddfe8d62-a7b7-4e30-a84d-91c92fc60bd0 stroke:#2c3143,stroke-width:4px;
  5["Query Tabular Select Peptides"];
  4 -->|output_psm| 5;
  6["Unipept pept2prot"];
  5 -->|output| 6;
  7["Unipept lca"];
  5 -->|output| 7;
  8["Go Pop2Prot DB"];
  2 -->|output| 8;
  6 -->|output_tsv| 8;
  6 -->|output_tsv| 8;
  4 -->|output_psm| 8;
  9["Genera | PSMs | Peptides"];
  4 -->|output_psm| 9;
  7 -->|output_tsv| 9;
  10["GO Terms: Biological Processes"];
  8 -->|sqlitedb| 10;
  11["GO Terms: Molecular Functions"];
  8 -->|sqlitedb| 11;
  12["GO Terms: Cellular Localization"];
  8 -->|sqlitedb| 12;

Inputs

Input Label
Input dataset Sixgill generated protein FASTA File
Input dataset collection Dataset Collection of Bering Strait MGF Files
Input dataset Gene Ontology Terms (Selected)

Outputs

From Output Label
Input dataset Sixgill generated protein FASTA File
Input dataset collection Dataset Collection of Bering Strait MGF Files
Input dataset Gene Ontology Terms (Selected)
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 Search GUI
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 Peptide Shaker
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular Query Tabular Select Peptides
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0 Unipept Unipept pept2prot
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0 Unipept Unipept lca
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular Go Pop2Prot DB
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular Genera | PSMs | Peptides
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 SQLite to tabular GO Terms: Biological Processes
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 SQLite to tabular GO Terms: Molecular Functions
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 SQLite to tabular GO Terms: Cellular Localization

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 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
10 aab73d220 2021-02-09 03:09:36 Update workflow.ga
9 1386c22b2 2021-02-09 01:36:59 Update workflow.ga
8 65c8cf73a 2021-02-04 21:18:44 Update workflow.ga
7 277c504ce 2021-02-04 21:14:34 Update workflow.ga
6 667ff3de9 2020-01-22 10:59:29 annotation
5 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
4 e4a786cd7 2019-02-19 13:08:55 Installing tools from workflows (#1269)
3 30b28d4c0 2017-12-03 15:44:21 broken workflow
2 2e53c11bf 2017-08-07 13:15:26 Update workflow
1 f6e08e286 2017-06-28 09:50:37 Metaproteomics tutorial (#393)

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaproteomics/workflows/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