GTN Proteogemics2 Database Search

proteomics-proteogenomics-dbsearch/galaxy-workflow-mouse-rnaseq-dbsearch

Author(s)

Version
7
Last updated
Feb 9, 2021
License
None Specified, defaults to CC-BY-4.0
Tags
proteomics

Features
Tutorial
Proteogenomics 2: Database Search
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00173
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nUniprot_cRAP_SAV_indel_translatedbed.FASTA"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nMGF Collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference Protein Accessions"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Search GUI"];
  0 -->|output| 3;
  1 -->|output| 3;
  d14f9481-80db-4c15-8afc-6fa38ef61deb["Output\nSearch GUI on input dataset(s)"];
  3 --> d14f9481-80db-4c15-8afc-6fa38ef61deb;
  style d14f9481-80db-4c15-8afc-6fa38ef61deb stroke:#2c3143,stroke-width:4px;
  4["Peptide Shaker"];
  3 -->|searchgui_results| 4;
  afe0f1a5-28bb-44bd-b32b-c634aa2154f3["Output\nPeptide Shaker on input dataset(s): mzidentML file"];
  4 --> afe0f1a5-28bb-44bd-b32b-c634aa2154f3;
  style afe0f1a5-28bb-44bd-b32b-c634aa2154f3 stroke:#2c3143,stroke-width:4px;
  5["mz to sqlite"];
  4 -->|mzidentML| 5;
  1 -->|output| 5;
  0 -->|output| 5;
  b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9["Output\nmz to sqlite on input dataset(s)"];
  5 --> b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9;
  style b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9 stroke:#2c3143,stroke-width:4px;
  6["Removing reference proteins"];
  4 -->|output_psm| 6;
  4 -->|output_psm| 6;
  2 -->|output| 6;
  a06ad5fa-9a00-4867-b976-3745c5e59c80["Output\nRemoving reference proteins"];
  6 --> a06ad5fa-9a00-4867-b976-3745c5e59c80;
  style a06ad5fa-9a00-4867-b976-3745c5e59c80 stroke:#2c3143,stroke-width:4px;
  7["Selecting sequence with length >6 and <30"];
  6 -->|output| 7;
  b71e5417-2864-4712-b5c1-c90725976baf["Output\nSelecting sequence with length >6 and <30"];
  7 --> b71e5417-2864-4712-b5c1-c90725976baf;
  style b71e5417-2864-4712-b5c1-c90725976baf stroke:#2c3143,stroke-width:4px;
  8["Peptides for BlastP analysis"];
  7 -->|output| 8;
  1ac3c776-8095-4db1-8518-3643dc081006["Output\nPeptides_for_BlastP_analysis"];
  8 --> 1ac3c776-8095-4db1-8518-3643dc081006;
  style 1ac3c776-8095-4db1-8518-3643dc081006 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Uniprot_cRAP_SAV_indel_translatedbed.FASTA
Input dataset collection MGF Collection
Input dataset Reference Protein Accessions

Outputs

From Output Label
Input dataset Uniprot_cRAP_SAV_indel_translatedbed.FASTA
Input dataset collection MGF Collection
Input dataset Reference Protein Accessions
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 Search GUI
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 Peptide Shaker
toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1 mz to sqlite
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular Removing reference proteins
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 Query Tabular Selecting sequence with length >6 and <30
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 Tabular-to-FASTA Peptides for BlastP analysis

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 View in ToolShed

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 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
8 6474a188d 2021-02-08 19:16:25 Update galaxy-workflow-mouse_rnaseq_dbsearch.ga
7 42e6b15fc 2021-01-27 21:17:51 Update galaxy-workflow-mouse_rnaseq_dbsearch.ga
6 801137308 2021-01-27 21:03:27 Update galaxy-workflow-mouse_rnaseq_dbsearch.ga
5 667ff3de9 2020-01-22 10:59:29 annotation
4 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
3 361236c41 2019-04-04 09:00:14 Changed format of workflows
2 6eef55b7e 2019-02-27 18:54:36 Updated install_tutorial_requirements.sh + minor fixes (#1275)
1 715d5f2ee 2018-11-20 20:46:19 fix folder names

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.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