reformatted and added comments

config.toml

-#This is a TOML Document
-#The TOML specification can be found here: https://github.com/toml-lang/toml
+# This is a TOML Document
+# The TOML specification can be found here: https://github.com/toml-lang/toml
 
-title="Abundance Parser Configuration"
+title = "Abundance Parser Configuration"
 
-#The input source and parsing parameters
+# The input source and parsing parameters
 [input]
-    #The CSV input file(s) to read data from
-    #The files should be of the same format (column titles,
-    #Example:
-    #input_files=[ "/input/file1",
-    #              path to file2
-    #             ]
-    input_files=["PATH_TO_INPUT_CSV"]
-    #fasta file(s) containing the protein sequence(s) to align against
-    prot_seq_fasta=["PATH_TO_FASTA_1","PATH_TO_FASTA_N"]
+# The CSV input file(s) to read data from.
+# The files should be of the same format (column titles,, modificatoin formatting, abundance column, fileID or
+# multiple abundance column. etc. If any aspects differ they should be run seperately
+# Example: input_files=[ "/input/file1", "path-to-file2"]
+input_files = [""]
+# path to fasta file(s) containing the protein sequence(s) to align against
+prot_seq_fasta = [""]
 
 
 [output]
-    #Relative or absolute path to desired output directory
-    output_directory="output/PATH_TO_OUTPUTSUBDIR"
+# Relative or absolute path to desired output directory
+output_directory = "output/"
 
-    #this stub is prepended by the file name of the input file
-    residue_output_name_stub="residueModificationAnalysis"
-    peptide_output_name_stub='peptideModificationAnalysis'
+# this stub is prepended by the file name of the input file
+residue_output_name_stub = "residueModAnalysis"
+peptide_output_name_stub = 'peptideModAnalysis'
 
-#Configuration of parser settings
+# Configuration of parser settings
 [parser_config]
-    sequence_column_title="Annotated Sequence"
-    #If false, files will be specified via abundance column
-    using_fileID_column=false
-    fileid_col_name="File ID"
-    #Title of column containing abundance. If using_fileID_column is set to
-    #true, only the first entry will be used
-    abundance_col_titles=["Abundance"]
-    calculate_peptide_modifications=true
-
-    [parser_config.regex]
-        regex_file="data/parser_regex.toml"
-        mod_parsing_regex="phosphoregex"
-        pos_master_regex="pos_master_regex"
-
-    [parser_config.master]
-        #Configs for use of pre-localized modification in master protein in
-        #parsing
-        use=false
-        #the name in the data of the master protein
-        master_protein_name= 'P10636-8'
-        master_protein_fasta_ID='sp|P10636-8|TAU_HUMAN'
-        #Column header containing the title of the column containing the
-        #localized modifications
-        modification_header="Modifications in Master Proteins"
+sequence_column_title = "Annotated Sequence"
+# If false, files will be specified via abundance column
+using_fileID_column = true
+fileid_col_name = "File ID"
+# Title of column containing abundance. If using_fileID_column is set to
+# true, only the first entry will be used
+abundance_col_titles = ["Precursor Abundance"]
+
+[parser_config.regex]
+regex_file = "data/parser_regex.toml"
+# phosphoregex for phosphorylation, ubiquitination for ubiquitination, etc. as defined in data/parser_regex.toml
+mod_parsing_regex = "phosphoregex"
+# the regex for parsing position in master protein, if needed. can be enabled in parser_config.master.use if needed
+pos_master_regex = "pos_master_regex"
+
+[parser_config.master]
+# Configs for use of pre-localized modification in master protein in parsing
+use = false
+#the name in the data of the master protein
+master_protein_name = 'P10636-8'
+master_protein_fasta_ID = 'sp|P10636-8|TAU_HUMAN'
+# Column header containing the title of the column containing the localized modifications
+modification_header = "Modifications in Master Proteins"
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