Tails Triple Dimethyl OpenMS2.1

proteomics-ntails/wf-ntails

Author(s)

version Version
4
last_modification Last updated
Jan 23, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
proteomics

Features

Tutorial
hands_on Detection and quantitation of N-termini (degradomics) via N-TAILS

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00165
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 Collection\nInput dataset collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FeatureFinderMultiplex"];
  0 -->|output| 2;
  3["HighResPrecursorMassCorrector"];
  2 -->|param_out_features| 3;
  0 -->|output| 3;
  4["MSGFPlusAdapter"];
  1 -->|output| 4;
  3 -->|param_out| 4;
  5["MSGFPlusAdapter"];
  1 -->|output| 5;
  3 -->|param_out| 5;
  6["MSGFPlusAdapter"];
  3 -->|param_out| 6;
  7["PeptideIndexer"];
  1 -->|output| 7;
  4 -->|param_out| 7;
  8["PeptideIndexer"];
  1 -->|output| 8;
  5 -->|param_out| 8;
  9["PeptideIndexer"];
  1 -->|output| 9;
  6 -->|param_out| 9;
  10["IDMerger"];
  7 -->|param_out| 10;
  8 -->|param_out| 10;
  9 -->|param_out| 10;
  11["ConsensusID"];
  10 -->|param_out| 11;
  12["PeptideIndexer"];
  1 -->|output| 12;
  11 -->|param_out| 12;
  13["FalseDiscoveryRate"];
  12 -->|param_out| 13;
  14["IDFilter"];
  13 -->|param_out| 14;
  15["IDMapper"];
  14 -->|param_out| 15;
  2 -->|param_out| 15;
  16["IDConflictResolver"];
  15 -->|param_out| 16;
  17["FileFilter"];
  16 -->|param_out| 17;
  18["FileMerger"];
  17 -->|param_out| 18;
  19["MzTabExporter"];
  18 -->|param_out| 19;

Inputs

Input Label
Input dataset collection
Input dataset

Outputs

From Output Label
Input dataset collection
Input dataset
FeatureFinderMultiplex FeatureFinderMultiplex
HighResPrecursorMassCorrector HighResPrecursorMassCorrector
MSGFPlusAdapter MSGFPlusAdapter
MSGFPlusAdapter MSGFPlusAdapter
MSGFPlusAdapter MSGFPlusAdapter
PeptideIndexer PeptideIndexer
PeptideIndexer PeptideIndexer
IDMerger IDMerger
ConsensusID ConsensusID
PeptideIndexer PeptideIndexer
IDFilter IDFilter
IDMapper IDMapper
IDConflictResolver IDConflictResolver
FileFilter FileFilter
FileMerger FileMerger
MzTabExporter MzTabExporter

Tools

Tool Links
ConsensusID
FalseDiscoveryRate
FeatureFinderMultiplex
FileFilter
FileMerger
HighResPrecursorMassCorrector
IDConflictResolver
IDFilter
IDMapper
IDMerger
MSGFPlusAdapter
MzTabExporter
PeptideIndexer

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 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 7da80b341 2020-01-10 14:56:15 Workflows fix
1 2c1271b67 2017-05-23 13:07:42 Restructure proteomics

For Admins

Installing the workflow tools

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