EncyclopeDIA-GTN 2.0
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Run on Galaxyencyclopedia- DIA Metaproteomics
Associated Tutorial
This workflows is part of the tutorial EncyclopeDIA, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): GalaxyP
Tutorial Author(s): Emma Leith, Subina Mehta, James Johnson, Pratik Jagtap, Timothy J. Griffin
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| BACKGROUND PROTEIN FASTA FILE | #main/BACKGROUND PROTEIN FASTA FILE | Input Protein Database file |
|
| EXPERIMENTAL DIA RAW FILES (WIDE) | #main/EXPERIMENTAL DIA RAW FILES (WIDE) | Input raw files |
|
| GPF DIA RAW Files (Dataset collection) | #main/GPF DIA RAW Files (Dataset collection) | encyclopedia- Gas phase fractionation files for library |
|
| SPECTRAL OR PROSIT LIBRARY | #main/SPECTRAL OR PROSIT LIBRARY | Library from Prosit |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Converting RAW to mzml | convert to mzml for encyclopedia toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 |
| 5 | msconvert | toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 |
| 6 | Library searching | Searching the mzml files against the Prosit library and the protein FASTA database. toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_searchtolib/encyclopedia_searchtolib/1.2.2+galaxy0 |
| 7 | EncyclopeDIA Quantify | toolshed.g2.bx.psu.edu/repos/galaxyp/encyclopedia_quantify/encyclopedia_quantify/1.2.2+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| CHROMATOGRAM LIBRARY | #main/CHROMATOGRAM LIBRARY | n/a |
|
| Experimental-dataset-MZML | #main/Experimental-dataset-MZML | n/a |
|
| GPF_MZML | #main/GPF_MZML | n/a |
|
| LOG | #main/LOG | n/a |
|
| PEPTIDE QUANTITATION OUTPUT | #main/PEPTIDE QUANTITATION OUTPUT | n/a |
|
| PROTEIN QUANTITATION OUTPUT | #main/PROTEIN QUANTITATION OUTPUT | n/a |
|
| QUANT LIBRARY | #main/QUANT LIBRARY | n/a |
|
| Quant-LOG | #main/Quant-LOG | n/a |
|
Version History
master
Creators and Submitter
Views: 1091 Downloads: 158 Runs: 0
Created: 2nd Jun 2025 at 10:54
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Teams: Galaxy Training Network
Organizations: Galaxy
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