Catchitt

name	comment	type
c	Conservative peaks (NarrowPeak file containing the conservative peaks)	FILE
r	Relaxed peaks (NarrowPeak file containing the relaxed peaks)	FILE
f	FAI of genome (FastA index file of the genome)	FILE
b	Bin width (The width of the genomic bins considered, valid range = [1, 10000], default = 50)	INT
rw	Region width (The width of the genomic regions considered for overlaps, valid range = [1, 10000], default = 50)	INT
outdir	The output directory, defaults to the current working directory (.)	STRING

name	comment	type
d	Data source (The format of the input file containing the coverage information, range={BAM/SAM, Bigwig}, default = BAM/SAM) Parameters for selection "BAM/SAM": i Input SAM/BAM (The input file containing the mapped DNase-seq/ATAC-seq reads) FILE Parameters for selection "Bigwig": i Input Bigwig (The input file containing the mapped DNase-seq/ATAC-seq reads) FILE f FastA index (The genome index) FILE
b	Bin width (The width of the genomic bins considered)	INT
outdir	The output directory, defaults to the current working directory (.)	STRING

name	comment	type
m	Motif model (The motif model in Dimont, HOCOMOCO, or Jaspar format, range={Dimont, HOCOMOCO, Jaspar}, default = Dimont) Parameters for selection "Dimont": d Dimont motif (Dimont motif model description) FILE Parameters for selection "HOCOMOCO": h HOCOMOCO PWM (PWM from the HOCOMOCO database) FILE Parameters for selection "Jaspar": j Jaspar PFM (PFM in Jaspar format) FILE
g	Genome (Genome as FastA file)	FILE
f	FAI of genome (FastA index file of the genome)	FILE
b	Bin width (The width of the genomic bins considered)	INT
l	Low-memory mode (Use slower mode with a smaller memory footprint, default = false)	BOOLEAN
outdir	The output directory, defaults to the current working directory (.)	STRING

name	comment	type
a	Accessibility (File containing accessibility features)	FILE
m	Motif (File containing motif features)	FILE
l	Labels (File containing the labels)	FILE
f	FAI of genome (FastA index file of the genome)	FILE
b	Bin width (The width of the genomic bins, valid range = [1, 1000], default = 50)	INT
n	Number of bins (The number of adjacent bins, valid range = [1, 20], default = 5)	INT
abb	Aggregation: bins before (The number of bins before the current one considered in the aggregation, valid range = [1, 20], default = 1)	INT
aba	Aggregation: bins after (The number of bins after the current one considered in the aggregation, valid range = [1, 20], default = 4)	INT
i	Iterations (The number of iterations of the interative training, valid range = [1, 20], default = 5)	INT
t	Training chromosomes (Training chromosomes, separated by commas, OPTIONAL)	STRING
itc	Iterative training chromosomes (Chromosomes with predictions in iterative training, separated by commas, OPTIONAL)	STRING
p	Percentile (Percentile of the prediction scores of positives used as threshold in iterative training, valid range = [0.0, 1.0], default = 0.99)	DOUBLE
outdir	The output directory, defaults to the current working directory (.)	STRING

name	comment	type
c	Classifiers (The classifiers trained by iterative training)	FILE
a	Accessibility (File containing accessibility features)	FILE
m	Motif (File containing motif features)	FILE
f	FAI of genome (FastA index file of the genome)	FILE
p	Prediction chromosomes (Prediction chromosomes, separated by commas, OPTIONAL)	STRING
abb	Aggregation: bins before (Number of bins before the current one considered for aggregation., OPTIONAL)	INT
aba	Aggregation: bins after (Number of bins after the current one considered for aggregation., OPTIONAL)	INT
n	Number of classifiers (Use only the first k classifiers for predictions., OPTIONAL)	INT
outdir	The output directory, defaults to the current working directory (.)	STRING