At line start argument must start by '>'
>input_folder='path/to/input/directory'
>output_folder='path/to/output/directory'

# Parallelization
>parallelization=False
>proc=5

# # Ontology_parse

>parse_ontology1=True
>parse_ontology2=False

# # # Ontology 1 # Only if parse_ontology1 == True
>file1='CELDA_import.owl'
>take_synonyms1=True
>filter_by_keywords1='human', 'mouse'
>ontologyName1=None
>synonym_type1='owlNCBITaxon:synonym'
>label_type1='CELDA:commonName xml:lang="en"', 'CELDA:commonName', 'rdfs:label'
>relative_type1='owl:someValuesFrom'
>file_clean_ontology1=''

# # # Ontology1 parsed path # only if parse_ontology1 == False
>ontology1_file=
>ontology1_name='CELDA'

# # # Ontology 2 # Only if parse_ontology2 == True
>file2=None
>take_synonyms2=True
>filter_by_keywords2='human', 'mouse'
>ontologyName2=None
>synonym_type2='owlNCBITaxon:synonym'
>label_type2='rdfs:label')
>relative_type2='owl:someValuesFrom'
>file_clean_ontology2=''

# # # Ontology2 parsed path # only if parse_ontology2 == False
>ontology2_file='Lifemap_parsed.ods'
>ontology2_name='Lifemap'

# # ontology_fusion
>del_old_trials_files=False
>onto1_fuseclasses=True
>onto2_fuseclasses=True
>onto1_restriction=False
>onto2_restriction=True
>onto1_list_clear='cell', 'cells'
>onto2_list_clear='cell', 'cells'
>synonyms=True
>text_process=True
>split_from1=
>split_since1=None
>split_from2=None
>split_since2=None
>windowsize=4
>globalthreshold=0.85
>localthreshold=0.7
>constriction_threshold=0.0
>topological_threshold=0.0
>topological_similarity='cosine'
