Merge pull request #602 from subinamehta/main

adding clinical metaproteomics workflows

workflows/proteomics/clinicalmp/clinicalmp-database-generation/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /iwc-clinicalmp-database-generation.ga
+  testParameterFiles:
+  - /iwc-clinicalmp-database-generation-tests.yml
+  authors:
+  - name: Subina Mehta
+    orcid: 0000-0001-9818-0537

workflows/proteomics/clinicalmp/clinicalmp-database-generation/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2024-11-18
+First release.

workflows/proteomics/clinicalmp/clinicalmp-database-generation/README.md

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+# Clinical Metaproteomics 1: Database Generation
+Metaproteomics involves the large-scale identification and analysis of all proteins expressed by microbiota. However, analyzing clinical samples using metaproteomics is complicated by the presence of abundant human (host) proteins, which can obscure the detection of less abundant microbial proteins.
+
+To overcome this challenge, we developed a metaproteomics workflow using tandem mass spectrometry (MS/MS) and bioinformatics tools on the Galaxy platform. This workflow enables the characterization of metaproteomes in clinical samples.
+
+The first step in this workflow is the Database Generation process. The Galaxy-P team has created a workflow that compiles a large database by downloading protein sequences of known disease-causing microorganisms. From this extensive database, a compact, relevant database is then created using the Metanovo tool.
+A GTN has been developed for this workflow. [https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html](https://training.galaxyproject.org/training-material/topics/proteomics/tutorials/clinical-mp-1-database-generation/tutorial.html)
+
+## Inputs dataset
+
+### Search Databases (FASTA) from [Zenodo](https://zenodo.org/records/14181725)
+- `HUMAN SwissProt Protein_Database.fasta`
+- `Species UniProt Protein Database FASTA.fasta`
+- `Contaminants (cRAP) Protein Database.fasta`
+
+### MSMS files download from [Zenodo](https://zenodo.org/records/14181725)
+- `PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.mgf`
+- `PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.mgf`
+- `PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.mgf`
+- `PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.mgf`
+
+## Input Values
+For Metanovo 
+- Peptide Length
+- Variable modifications
+- Labeled element
+
+## Processing
+- Merge all the resultant FASTA files

workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation-tests.yml

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+- doc: Test outline for iwc-clinicalmp-database-generation
+  job:
+    Human SwissProt Protein Database:
+      class: File
+      location: https://zenodo.org/records/14181725/files/HUMAN-SwissProt-Protein-Database.fasta?download=1
+      filetype: fasta
+    Species UniProt Protein Database:
+      class: File
+      location: https://zenodo.org/records/14181725/files/Species_UniProt_FASTA.fasta?download=1
+      filetype: fasta
+    Contaminants cRAP Protein Database:
+      class: File
+      location: https://zenodo.org/records/14181725/files/Contaminants(cRAP)-Protein-Database.fasta?download=1
+      filetype: fasta
+    Tandem Mass Spectrometry (MS/MS) datasets:
+      class: Collection
+      collection_type: list
+      elements:
+        - class: File
+          identifier: PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.mgf
+          location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F15_9Aug19_Rage_Rep-19-06-08.mgf?download=1
+        - class: File
+          identifier: PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.mgf
+          location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F13_9Aug19_Rage_Rep-19-06-08.mgf?download=1
+        - class: File
+          identifier: PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.mgf
+          location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F11_9Aug19_Rage_Rep-19-06-08.mgf?download=1
+        - class: File
+          identifier: PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.mgf
+          location: https://zenodo.org/records/14181725/files/PTRC_Skubitz_Plex2_F10_9Aug19_Rage_Rep-19-06-08.mgf?download=1
+  outputs:
+    Human UniProt Microbial Proteins cRAP for MetaNovo:
+      asserts:
+        - that: has_text
+          text: ">sp|"
+    Metanovo Compact database:
+      asserts:
+        - that: has_text
+          text: ">sp|"
+    Metanovo Compact CSV database:
+      asserts:
+        - that: has_text
+          text: "index"
+    Human UniProt Microbial Proteins from MetaNovo cRAP:
+      asserts:
+        - that: has_text
+          text: ">sp|"