clinicalmp-discovery/main v0.1
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Workflow Type: Galaxy
Frozen
Workflow for clinical metaproteomics database searching
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Experimental Design Discovery MaxQuant | Experimental Design Discovery MaxQuant | File for experimental design containing Name, Fraction, Experiment, and PTM, where the name refers to the dataset filename, with each dataset listed on a separate line. |
|
| Human UniProt Microbial Proteins from MetaNovo and cRAP | Human UniProt Microbial Proteins from MetaNovo and cRAP | n/a |
|
| Tandem Mass Spectrometry MSMS files | Tandem Mass Spectrometry MSMS files | Input Raw files |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | IdentificationParameters:PAR file | identification parameters for SGPS toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/4.0.41+galaxy1 |
| 3 | Human SwissProt | toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4 |
| 4 | Contaminants | toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.4 |
| 6 | FastaCLI_ MetaNovo Human SwissProt cRAP with decoys | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/fasta_cli/4.0.41+galaxy1 |
| 7 | msconvert | toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2 |
| 8 | Human SwissProt+cRAP | toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 |
| 9 | MaxQuant | toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/2.0.3.0+galaxy0 |
| 10 | Search GUI | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.41+galaxy1 |
| 11 | FASTA to Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0 |
| 12 | Select microbial peptides MQ | Grep1 |
| 13 | Peptide Shaker | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.33+galaxy1 |
| 14 | Filtering Accesions | toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.0 |
| 15 | MQ Peptide Sequences | Cut1 |
| 16 | Select microbial peptides SGPS | Grep1 |
| 17 | Select microbial PSMs SGPS | Grep1 |
| 18 | Remove beginning from MQ Peptides | Remove beginning1 |
| 19 | Filter confident microbial Peptides | Filter1 |
| 20 | Filter confident microbial PSMs | Filter1 |
| 21 | MQ Distinct Peptides | Grouping1 |
| 22 | Extracting peptides SGPS from PSM | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.0 |
| 23 | Cut Peptide column | Cut1 |
| 24 | SGPS Distinct Peptides | Grouping1 |
| 25 | SGPS MQ Peptides | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 26 | Distinct Peptides | Grouping1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Human SwissProt | Human SwissProt | n/a |
|
| Human SwissProt+cRAP | Human SwissProt+cRAP | n/a |
|
| Select microbial peptides MQ | Select microbial peptides MQ | n/a |
|
| Filtering Accessions | Filtering Accessions | n/a |
|
| MQ Peptide Sequences | MQ Peptide Sequences | n/a |
|
| Select microbial peptides SGPS | Select microbial peptides SGPS | n/a |
|
| Select microbial PSMs SGPS | Select microbial PSMs SGPS | n/a |
|
| Header removed MQ Peptides | Header removed MQ Peptides | n/a |
|
| Filter confident microbial Peptides | Filter confident microbial Peptides | n/a |
|
| Filter confident microbial PSMs | Filter confident microbial PSMs | n/a |
|
| MQ Distinct Peptides | MQ Distinct Peptides | n/a |
|
| Extracting peptides SGPS from PSM | Extracting peptides SGPS from PSM | n/a |
|
| SGPS Peptides | SGPS Peptides | n/a |
|
| SGPS Distinct Peptides | SGPS Distinct Peptides | n/a |
|
| SGPS MQ Peptides | SGPS MQ Peptides | n/a |
|
| Distinct Peptides | Distinct Peptides | n/a |
|
Version History
v0.1 (earliest) Created 10th Dec 2024 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.104fac0e
Creators and Submitter
Activity
Views: 2251 Downloads: 1595 Runs: 2
Created: 10th Dec 2024 at 03:02
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