Proteomics: Peptide and Protein Quantification via stable istobe labeling
proteomics-protein-quant-sil/workflow
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flowchart TD 0["ℹ️ Input Dataset\nmzml raw file"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nfasta file"]; style 1 stroke:#2c3143,stroke-width:4px; 2["FeatureFinderMultiplex"]; 0 -->|output| 2; 3["XTandemAdapter"]; 1 -->|output| 3; 0 -->|output| 3; 4["FileInfo"]; 3 -->|out| 4; 5["PeptideIndexer"]; 1 -->|output| 5; 3 -->|out| 5; 6["IDPosteriorErrorProbability"]; 5 -->|out| 6; 7["FalseDiscoveryRate"]; 6 -->|out| 7; 8["IDScoreSwitcher"]; 7 -->|out| 8; 9["FileInfo"]; 8 -->|out| 9; 10["FidoAdapter"]; 8 -->|out| 10; 11["FalseDiscoveryRate"]; 10 -->|out| 11; 12["FileInfo"]; 11 -->|out| 12; 13["TextExporter"]; 11 -->|out| 13; 14["IDMapper"]; 11 -->|out| 14; 2 -->|out_multiplets| 14; 15["Select"]; 13 -->|out| 15; 16["Select"]; 13 -->|out| 16; 17["IDConflictResolver"]; 14 -->|out| 17; 18["MultiplexResolver"]; 17 -->|out| 18; 19["ProteinQuantifier"]; 18 -->|out| 19; 11 -->|out| 19; 20["Summary Statistics"]; 19 -->|out| 20; 21["Select last"]; 19 -->|out| 21; 22["Histogram"]; 21 -->|outfile| 22;
Inputs
Input | Label |
---|---|
Input dataset | mzml raw file |
Input dataset | fasta file |
Outputs
From | Output | Label |
---|---|---|
Input dataset | mzml raw file | |
Input dataset | fasta file | |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0 | FeatureFinderMultiplex | |
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 | |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.6+galaxy0 | IDMapper | |
Grep1 | Select | |
Grep1 | Select | |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.6+galaxy0 | IDConflictResolver | |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.5+galaxy0 | MultiplexResolver | |
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.6+galaxy0 | ProteinQuantifier | |
Summary_Statistics1 | Summary Statistics | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0 | Select last | |
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4 | Histogram |
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 |
---|---|---|---|
11 | 54b4d9fcc | 2020-11-01 09:56:40 | Adding tags to workflows |
10 | ca84d7395 | 2020-10-31 20:41:54 | Updating Tutorials to OpenMS 2.6, adjusting of parameters and tools, adding tool versions |
9 | c5002c655 | 2020-10-03 01:31:21 | protein-quant-sil |
8 | 667ff3de9 | 2020-01-22 10:59:29 | annotation |
7 | eb4d724e0 | 2020-01-15 10:41:35 | Workflow renaming |
6 | e42145c47 | 2019-03-20 15:35:21 | Updated workflow |
5 | 3a0757df3 | 2017-11-29 14:44:30 | Enabled FFMult advanced options without changing any parameter |
4 | 66e504fe2 | 2017-11-28 11:17:13 | Workaround for ProteinQuantifier bug: changed '-include_all' to TRUE |
3 | ed8674c45 | 2017-11-28 10:45:52 | Updated workflow parameters |
2 | c7d698525 | 2017-06-08 16:12:42 | Fill workflow file with an empty workflow |
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/protein-quant-sil/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