Metaproteomics_GTN

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Workflow Type: Galaxy

Metaproteomics tutorial

Associated Tutorial

This workflows is part of the tutorial Metaproteomics_GTN, available in the GTN

Thanks to...

Tutorial Author(s): Timothy J. Griffin, Pratik Jagtap, James Johnson, Clemens Blank, Subina Mehta

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1159?version=1

Inputs

ID Name Description Type
Dataset Collection of Bering Strait MGF Files #main/Dataset Collection of Bering Strait MGF Files n/a
  • array containing
    • File
Gene Ontology Terms (Selected) #main/Gene Ontology Terms (Selected) n/a
  • File
Sixgill generated protein FASTA File #main/Sixgill generated protein FASTA File n/a
  • File

Steps

ID Name Description
3 Search GUI toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1
4 Peptide Shaker toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3
5 Query Tabular Select Peptides toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
6 Unipept pept2prot toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0
7 Unipept lca toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0
8 Go Pop2Prot DB toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
9 Genera | PSMs | Peptides toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
10 GO Terms: Biological Processes toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0
11 GO Terms: Molecular Functions toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0
12 GO Terms: Cellular Localization toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0

Outputs

ID Name Description Type
Peptide Shaker on input dataset(s): mzidentML file #main/Peptide Shaker on input dataset(s): mzidentML file n/a
  • File
Search GUI on input dataset(s) #main/Search GUI on input dataset(s) n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_15 #main/_anonymous_output_15 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

7.0 (latest) Created 16th Jul 2024 at 14:07 by Helena Rasche

Added/updated 4 files


Open master 491c7b5

9.0 (earliest) Created 25th Jun 2024 at 11:04 by Helena Rasche

Added/updated 4 files


Frozen 9.0 5b2556e
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tool
Unipept
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 1532   Downloads: 656   Runs: 0

Created: 25th Jun 2024 at 11:04

Last updated: 25th Jun 2024 at 11:04

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Total size: 138 KB
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