GigaScience_Database_merge_FragPipe_STS26T_demonstration
proteomics-neoantigen-3-fragpipe-discovery/main-workflow
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flowchart TD 0["ℹ️ Input Dataset\nHuman_cRAP_Non_normal_transcripts_dB"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nFusion-database"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nInput-RAW-FILE"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nFragPipe_Experimental_design_tabular"]; style 3 stroke:#2c3143,stroke-width:4px; 4["Merge_non-normal_fusion_FASTA-files"]; 0 -->|output| 4; 1 -->|output| 4; 19df6de4-6440-4693-b893-139213d4e07e["Output\nNon_normal_and_Fusion_dB"]; 4 --> 19df6de4-6440-4693-b893-139213d4e07e; style 19df6de4-6440-4693-b893-139213d4e07e stroke:#2c3143,stroke-width:4px; 5["Validation_of_Fasta_file"]; 4 -->|output| 5; efefe5f3-7bb9-42fe-a39b-b220fcaf1add["Output\nValidated-fasta"]; 5 --> efefe5f3-7bb9-42fe-a39b-b220fcaf1add; style efefe5f3-7bb9-42fe-a39b-b220fcaf1add stroke:#2c3143,stroke-width:4px; 6["Fragpipe"]; 5 -->|goodFastaOut| 6; 2 -->|output| 6; 3 -->|output| 6; 6e4e993f-8d69-4008-9528-91ea2699ab02["Output\nFragpipe_output_protein"]; 6 --> 6e4e993f-8d69-4008-9528-91ea2699ab02; style 6e4e993f-8d69-4008-9528-91ea2699ab02 stroke:#2c3143,stroke-width:4px; b1ac88a6-70fb-4a0c-bc52-aa4f37019c8d["Output\nFragpipe_output_psm"]; 6 --> b1ac88a6-70fb-4a0c-bc52-aa4f37019c8d; style b1ac88a6-70fb-4a0c-bc52-aa4f37019c8d stroke:#2c3143,stroke-width:4px; 80182cb4-4a70-4a50-a42f-0de196f6e95b["Output\nFragpipe_output_peptide"]; 6 --> 80182cb4-4a70-4a50-a42f-0de196f6e95b; style 80182cb4-4a70-4a50-a42f-0de196f6e95b stroke:#2c3143,stroke-width:4px; 7["Extract_Peptides_from_Fragpipe"]; 6 -->|output_peptide| 7; a3548299-ee6a-4649-a741-0e934557daf3["Output\nFragpipe-Peptide-Report"]; 7 --> a3548299-ee6a-4649-a741-0e934557daf3; style a3548299-ee6a-4649-a741-0e934557daf3 stroke:#2c3143,stroke-width:4px; 8["Removing_known_human_peptides"]; 7 -->|output| 8; 190bb3e5-3359-4ac3-9515-055fe73926da["Output\nRemoving_known_human_peptides_and_contaminants"]; 8 --> 190bb3e5-3359-4ac3-9515-055fe73926da; style 190bb3e5-3359-4ac3-9515-055fe73926da stroke:#2c3143,stroke-width:4px; 9["Extracting_NeoAntigen_Peptides_for_PepQuery"]; 8 -->|out_file1| 9; 848d90aa-2d7e-4a96-8918-57efa8705dc1["Output\nNeoantigen_Peptide_Candidates_for_PepQuery"]; 9 --> 848d90aa-2d7e-4a96-8918-57efa8705dc1; style 848d90aa-2d7e-4a96-8918-57efa8705dc1 stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | Human_cRAP_Non_normal_transcripts_dB |
Input dataset | Fusion-database |
Input dataset | Input-RAW-FILE |
Input dataset | FragPipe_Experimental_design_tabular |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 | FASTA Merge Files and Filter Unique Sequences | Merge_non-normal_fusion_FASTA-files |
toolshed.g2.bx.psu.edu/repos/galaxyp/validate_fasta_database/validate_fasta_database/0.1.5 | Validate FASTA Database | Validation_of_Fasta_file |
toolshed.g2.bx.psu.edu/repos/galaxyp/fragpipe/fragpipe/20.0+galaxy2 | FragPipe - Academic Research and Education User License (Non-Commercial) | Fragpipe |
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 | Collapse Collection | Extract_Peptides_from_Fragpipe |
Grep1 | Select | Removing_known_human_peptides |
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 | Query Tabular | Extracting_NeoAntigen_Peptides_for_PepQuery |
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:
Version History
Version | Commit | Time | Comments |
---|---|---|---|
1 | 6e4ce4916 | 2024-11-14 15:41:21 | Made sure the order is right |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/neoantigen-3-fragpipe-discovery/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