{"name":["mutated_peptide_generator"],"version":"1.1","necessary_parameters":[{"key":"input_vcf_text","display_name":"Input Variant Calls (VCF)","type":"str","description":"Input Variant Calls (VCF)","example_input":"##fileformat=VCFv4.1\n##fileDate=20240220\n..."}],"optional_parameters":[{"key":"annotate","display_name":"Annotate","type":"bool","description":"annotate the VCF with SNPeff ","default":false,"example_input":true},{"key":"reference_genome","display_name":"Reference Genome","type":"string","enum":["GRCh38","GRCh37","GRCm38"],"description":"Reference Genome","default":"GRCh38","example_input":"GRCh38"},{"key":"peptide_length","display_name":"Peptide Length","type":"int","description":"The number of amino acids in the peptide","default":21,"example_input":21},{"key":"frameshift_overlap","display_name":"Frameshift Overlap","type":"int","description":"Frameshift mutations often result in a relatively long stretch of amino acids that are different from the reference. Maximum allowed value is peptide length minus one; the UI should cap this control when peptide length changes.","default":9,"example_input":9,"value_limits":{"min":1,"max":"peptide_length - 1"}},{"key":"peptide_mutation_position1","display_name":"Peptide 1 Mutation Position","type":"int","description":"Position in the peptide where the mutation should be located.","default":"peptide_length // 2","example_input":10},{"key":"peptide_mutation_position2","display_name":"Peptide 2 Mutation Position","type":"int","description":"An additional peptide for a given variant with the SNP at a different position","default":null,"example_input":null},{"key":"maximum_peptide_length","display_name":"Maximum Peptide Length","type":"int","description":"The maximum peptide length if creating a peptide longer than the \"Peptide Length\" parameter may be desirable. May equal peptide length (minimum) or up to peptide length + 10.","default":"peptide_length + 3","example_input":24}],"reference_genomes":[{"short_name":"GRCh38","display_name":"GRCh38"},{"short_name":"GRCh37","display_name":"GRCh37"},{"short_name":"GRCm38","display_name":"GRCm38(mm10)"}]}