"""
script_info["required_options"] = [
make_option(
"-f", "--forward_reads_fp", type="existing_filepath", help="Path to input forward reads in FASTQ format."
),
make_option(
"-r", "--reverse_reads_fp", type="existing_filepath", help="Path to input reverse reads in FASTQ format."
),
make_option("-o", "--output_dir", type="new_dirpath", help="Directory to store result files"),
]
script_info["optional_options"] = [
make_option(
"-m",
"--pe_join_method",
type="choice",
choices=list(join_method_names.keys()),
help="Method to use for joining paired-ends. Valid choices"
+ " are: "
+ ", ".join(join_method_names.keys())
+ " [default: %default]",
default="fastq-join",
),
make_option(
"-b",
"--index_reads_fp",
type="existing_filepath",
help="Path to the barcode / index reads in FASTQ format." " Will be filtered based on surviving joined pairs.",
),
make_option(
"-j",
"--min_overlap",
type="existing_filepath",
help='Path to input forward reads in FASTQ format.'),
make_option('-r',
'--reverse_reads_fp',
type="existing_filepath",
help='Path to input reverse reads in FASTQ format.'),
make_option('-o',
'--output_dir',
type='new_dirpath',
help='Directory to store result files')
]
script_info['optional_options'] = [
make_option('-m',
'--pe_join_method',
type='choice',
choices=list(join_method_names.keys()),
help='Method to use for joining paired-ends. Valid choices' +
' are: ' + ', '.join(join_method_names.keys()) +
' [default: %default]',
default='fastq-join'),
make_option('-b',
'--index_reads_fp',
type='existing_filepath',
help='Path to the barcode / index reads in FASTQ format.'
' Will be filtered based on surviving joined pairs.'),
make_option(
'-j',
'--min_overlap',
type='int',
help='Applies to both fastq-join and SeqPrep methods.' +
' Minimum allowed overlap in base-pairs required to join pairs.' +
conjunction with the joined
paired-ends file as input to split_libraries_fastq.py. Except for
missing reads that may result from failed merging of paired-ends, the
index-reads and joined-reads must be in the same order.
"""
script_info['required_options'] = [
make_option('-f', '--forward_reads_fp', type="existing_filepath",
help='Path to input forward reads in FASTQ format.'),
make_option('-r', '--reverse_reads_fp', type="existing_filepath",
help='Path to input reverse reads in FASTQ format.'),
make_option('-o', '--output_dir', type='new_dirpath',
help='Directory to store result files')]
script_info['optional_options'] = [
make_option('-m', '--pe_join_method', type='choice',
choices=list(join_method_names.keys()),
help='Method to use for joining paired-ends. Valid choices' +
' are: ' + ', '.join(join_method_names.keys()) +
' [default: %default]', default='fastq-join'),
make_option('-b', '--index_reads_fp', type='existing_filepath',
help='Path to the barcode / index reads in FASTQ format.'
' Will be filtered based on surviving joined pairs.'),
make_option('-j', '--min_overlap', type='int',
help='Applies to both fastq-join and SeqPrep methods.' +
' Minimum allowed overlap in base-pairs required to join pairs.' +
' If not set, progam defaults will be used.'
' Must be an integer. [default: %default]', default=None),
make_option('-p', '--perc_max_diff', type='int',
help='Only applies to fastq-join method, otherwise ignored. ' +
'Maximum allowed % differences within region of overlap.' +
' If not set, progam defaults will be used.' +