metaQuantome_datacreation_workflow
proteomics-metaquantome-data-creation/main-workflow
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flowchart TD 0["ℹ️ Input Collection\nInput dataset collection"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nExperiment_Design"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nFASTA_db"]; style 2 stroke:#2c3143,stroke-width:4px; 3["mzml to mgf"]; 0 -->|output| 3; 4["Search GUI"]; 2 -->|output| 4; 3 -->|output| 4; 5["Peptide Shaker"]; 4 -->|searchgui_results| 5; 6["Replace Text"]; 5 -->|output_psm| 6; 7["Remove beginning"]; 5 -->|output_peptides| 7; 8["Unipept_lca"]; 5 -->|output_peptides| 8; 9["FlashLFQ"]; 1 -->|output| 9; 6 -->|outfile| 9; 0 -->|output| 9; 10["Unipept_peptinfo"]; 7 -->|out_file1| 10; 11["Replace Text"]; 8 -->|output_tsv| 11; 12["Regex Find And Replace"]; 9 -->|quantifiedPeptides| 12; 13["selecting EC column"]; 10 -->|output_ec_tsv| 13; 14["filter 5% All_funct"]; 10 -->|output_go_tsv| 14; 15["GO_EC"]; 13 -->|out_file1| 15; 16["GO_BP"]; 14 -->|output| 16; 17["GO_CC"]; 14 -->|output| 17; 18["GO_MF"]; 14 -->|output| 18;
Inputs
Input | Label |
---|---|
Input dataset collection | |
Input dataset | Experiment_Design |
Input dataset | FASTA_db |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0 | msconvert | mzml to mgf |
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 | Peptide Shaker | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 | Replace Text | |
toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/1.0.3.0 | FlashLFQ | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 | Replace Text | |
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0 | Regex Find And Replace | |
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 | Query Tabular | filter 5% (All_funct) |
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 | Query Tabular | GO_EC |
Filter1 | Filter | GO_BP |
Filter1 | Filter | GO_CC |
Filter1 | Filter | GO_MF |
Tools
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 |
---|---|---|---|
14 | 72e53ea9a | 2021-11-10 18:44:34 | Rename workflow.ga to main_workflow.ga |
13 | b63d3bd07 | 2021-11-10 18:06:54 | Rename main_workflow.ga to workflow.ga |
12 | 02a2548ec | 2021-11-09 16:10:35 | Update main_workflow.ga |
11 | d4a710e9f | 2021-11-09 16:04:54 | Update main_workflow.ga |
10 | d0478e7ff | 2021-11-09 16:00:03 | Update main_workflow.ga |
9 | 2c4ad397f | 2020-10-16 19:41:28 | Fixed tool_state. |
8 | f81d5946b | 2020-10-16 18:41:38 | Added collection to test. |
7 | 70b86ecbf | 2020-10-16 17:52:11 | Updated workflow. |
6 | b8a5ce3d4 | 2020-10-15 23:04:35 | Update main_workflow.ga |
5 | 71d516d05 | 2020-10-15 19:30:59 | Update main_workflow.ga |
4 | aa695993e | 2020-10-12 12:59:36 | Update main_workflow.ga |
3 | dadb44fb5 | 2020-10-12 02:21:26 | Update main_workflow.ga |
2 | a45af5ea9 | 2020-10-12 02:20:38 | Update main_workflow.ga |
1 | c042f2b71 | 2020-09-17 15:49:53 | planemo workflow-to-tutorial |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/metaquantome-data-creation/workflows/main_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