Workflows

These workflows are associated with MaxQuant and MSstats for the analysis of label-free data

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.

Proteomics: MaxQuant and MSstats LFQ workflow

Last updated Jun 4, 2021

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nannotation file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncomparison matrix"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nfasta protein database"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Collection\nraw files"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["MaxQuant"];
  2 -->|output| 4;
  3 -->|output| 4;
  5["Select"];
  4 -->|proteinGroups| 5;
  6["Select"];
  4 -->|evidence| 6;
  7["Replace Text"];
  5 -->|out_file1| 7;
  8["Replace Text"];
  6 -->|out_file1| 8;
  9["MSstats"];
  1 -->|output| 9;
  0 -->|output| 9;
  8 -->|outfile| 9;
  7 -->|outfile| 9;
  10["Datamash"];
  9 -->|runlevel_data| 10;
  11["Summary Statistics"];
  9 -->|runlevel_data| 11;
  12["Replace Text"];
  9 -->|comparison_result| 12;
  13["Replace Text"];
  9 -->|quant_sample_matrix| 13;
  14["Filter"];
  12 -->|outfile| 14;
  15["Filter"];
  14 -->|out_file1| 15;
  16["Filter"];
  14 -->|out_file1| 16;
  17["Filter"];
  15 -->|out_file1| 17;
  18["Filter"];
  16 -->|out_file1| 18;
  19["Cut"];
  17 -->|out_file1| 19;
  20["Cut"];
  18 -->|out_file1| 20;
  21["Join"];
  13 -->|outfile| 21;
  19 -->|out_file1| 21;
  22["Join"];
  13 -->|outfile| 22;
  20 -->|out_file1| 22;
  23["heatmap2"];
  21 -->|output| 23;
  24["UniProt"];
  21 -->|output| 24;
  25["heatmap2"];
  22 -->|output| 25;
  26["UniProt"];
  22 -->|output| 26;
  27["FASTA-to-Tabular"];
  24 -->|outfile_retrieve_fasta| 27;
  28["FASTA-to-Tabular"];
  26 -->|outfile_retrieve_fasta| 28;

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: