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

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
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Views: 416   Downloads: 150

Created: 25th Jun 2024 at 11:04

Last updated: 25th Jun 2024 at 11:04

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