Peptide And Protein ID Via OMS Using Two Search Engines

proteomics-protein-id-oms/workflow-two-search-engines

Author(s)

Version
4
Last updated
Jan 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Peptide and Protein ID using OpenMS tools
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00168
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nmzML_test_dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nHuman_database_including_decoys"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["XTandemAdapter"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["MSGFPlusAdapter"];
  1 -->|output| 3;
  4["IDPosteriorErrorProbability"];
  2 -->|param_out| 4;
  5["IDPosteriorErrorProbability"];
  3 -->|param_out| 5;
  6["IDMerger"];
  5 -->|param_out| 6;
  4 -->|param_out| 6;
  7["ConsensusID"];
  6 -->|param_out| 7;
  8["PeptideIndexer"];
  1 -->|output| 8;
  7 -->|param_out| 8;
  9["FalseDiscoveryRate"];
  8 -->|param_out| 9;
  10["IDScoreSwitcher"];
  9 -->|param_out| 10;
  11["FileInfo"];
  9 -->|param_out| 11;
  12["FidoAdapter"];
  10 -->|param_out| 12;
  13["FalseDiscoveryRate"];
  12 -->|param_out| 13;
  14["IDFilter"];
  13 -->|param_out| 14;
  15["FileInfo"];
  14 -->|param_out| 15;

Inputs

Input Label
Input dataset mzML_test_dataset
Input dataset Human_database_including_decoys

Outputs

From Output Label
Input dataset mzML_test_dataset
Input dataset Human_database_including_decoys
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0 FalseDiscoveryRate
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0 FileInfo
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0 IDFilter
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0 FileInfo

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1 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
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 643fab24d 2018-10-02 22:20:38 update workflow
1 b916508e1 2017-11-14 10:39:37 Added workflow for two search engines, deleted ms2 PeakPicking and updated old workflow, added link to workflow in tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/protein-id-oms/workflows/workflow_two-search-engines.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