## templated variables to be replaced exist as <__var_name__>

# database settings
DATABASE=/suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/training/pasa/Plecoglossus_altivelis_pasa

#######################################################
# Parameters to specify to specific scripts in pipeline
# create a key = "script_name" + ":" + "parameter" 
# assign a value as done above.


#script cDNA_annotation_comparer.dbi
cDNA_annotation_comparer.dbi:--MIN_PERCENT_OVERLAP=<__MIN_PERCENT_OVERLAP__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_PROT_CODING=<__MIN_PERCENT_PROT_CODING__>
cDNA_annotation_comparer.dbi:--MIN_PERID_PROT_COMPARE=<__MIN_PERID_PROT_COMPARE__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_LENGTH_FL_COMPARE=<__MIN_PERCENT_LENGTH_FL_COMPARE__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_LENGTH_NONFL_COMPARE=<__MIN_PERCENT_LENGTH_NONFL_COMPARE__>
cDNA_annotation_comparer.dbi:--MIN_FL_ORF_SIZE=<__MIN_FL_ORF_SIZE__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_ALIGN_LENGTH=<__MIN_PERCENT_ALIGN_LENGTH__>
cDNA_annotation_comparer.dbi:--MIN_PERCENT_OVERLAP_GENE_REPLACE=<__MIN_PERCENT_OVERLAP_GENE_REPLACE__>
cDNA_annotation_comparer.dbi:--STOMP_HIGH_PERCENTAGE_OVERLAPPING_GENE=<__STOMP_HIGH_PERCENTAGE_OVERLAPPING_GENE__>
cDNA_annotation_comparer.dbi:--TRUST_FL_STATUS=<__TRUST_FL_STATUS__>
cDNA_annotation_comparer.dbi:--MAX_UTR_EXONS=<__MAX_UTR_EXONS__>
cDNA_annotation_comparer.dbi:--GENETIC_CODE=<__GENETIC_CODE__>