Create lcms-v2.2.yaml

Changed lab_processed/ , lab_processed/ID_search_results/  and lab_processed/ID_metadata/  directories to optional.

src/ingest_validation_tools/directory-schemas/lcms-v2.2.yaml

@@ -0,0 +1,50 @@
+files:
+  -
+    pattern: extras\/.*
+    required: True
+    description: Folder for general lab-specific files related to the dataset.
+  -
+    pattern: extras\/mass-spec_environment\.(?:json|tsv)
+    required: False
+    description: JSON or TSV file containing the machine parameters/settings. This is akin to the microscope_environment.json file that's used to describe the imaging equipment.
+  -
+    pattern: raw\/.*
+    required: True
+    description: Raw data files for the experiment.
+  -  
+    pattern: raw\/[^\/]+\.raw
+    required: True
+    description: Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans.
+    example: raw/20200707_rmi049_75umPLRPS_Kidney_GF10pc_VAN0003LK32_biorep05_techrep02.raw
+  -  
+    pattern: raw\/[^\/]+\.(?:mzML|d)
+    required: True
+    description: Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans.
+  -
+    pattern: lab_processed\/.*
+    required: False
+    description: Lab processed files
+  -
+    pattern: lab_processed\/ID_search_results\/.*
+    required: False
+    description: Identification results. 
+  -
+    pattern: lab_processed\/ID_search_results\/[^\/]+\.csv
+    required: False
+    description: Annotated data describing (qualitative or quantitative) the proteins, metabolites, lipids, peptides, phosphopeptides, or glycans identified from the corresponding raw data. In the case of MS1 this file should include a list of features.
+  -
+    pattern: lab_processed\/ID_metadata\/.*
+    required: False
+    description: Identification search parameters/metadata.
+  -
+    pattern: lab_processed\/ID_metadata\/[^\/]+\.csv
+    required: False
+    description: Software settings used during the analyte identification process (e.g., from MaxQuant or Proteome Discoverer).
+  -
+    pattern: lab_processed\/QC_results\/.*
+    required: False
+    description: Output file resulting from QC analysis.
+  -
+    pattern: lab_processed\/QC_results\/[^\/]+\.txt
+    required: False
+    description: A list of metrics with the score of the current dataset that shows the quality of data collection.