Proteomics: Peptide and Protein ID using OpenMS

proteomics-protein-id-oms/workflow

Author(s)

Version
6
Last updated
Nov 1, 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:W00167
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
param_out
out
output
out
out
out
out
out
out
out
out
out
out
out
ℹ️ Input Dataset
mzml input
ℹ️ Input Dataset
fasta input
PeakPickerHiRes
XTandemAdapter
FileInfo
PeptideIndexer
IDPosteriorErrorProbability
FalseDiscoveryRate
IDScoreSwitcher
FileInfo
FidoAdapter
FalseDiscoveryRate
FileInfo
TextExporter
Select
Select

Inputs

Input Label
Input dataset mzml input
Input dataset fasta input

Outputs

From Output Label
Input dataset mzml input
Input dataset fasta input
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0 PeakPickerHiRes
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+galaxy0 XTandemAdapter
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0 FileInfo
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0 PeptideIndexer
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0 IDPosteriorErrorProbability
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0 FalseDiscoveryRate
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0 IDScoreSwitcher
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0 FileInfo
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0 FidoAdapter
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0 FalseDiscoveryRate
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0 FileInfo
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0 TextExporter
Grep1 Select
Grep1 Select

Tools

Tool Links
Grep1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.6+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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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
9 54b4d9fcc 2020-11-01 09:56:40 Adding tags to workflows
8 ca84d7395 2020-10-31 20:41:54 Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions
7 667ff3de9 2020-01-22 10:59:29 annotation
6 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
5 775a0b425 2019-03-20 14:30:01 Updated workflow containing all follow up tools
4 08f1e0dc3 2019-03-20 13:36:19 Updated workflow for ID training
3 dbcc48eaa 2017-11-14 16:43:10 fix workflow name
2 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
1 a6411f26e 2017-10-16 10:13:27 New tutorial "Protein ID using OpenMS" and major revision of "Protein ID using SG/PS" (#570)

For Admins

Installing the workflow tools

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