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name: circosight
version: "0.1.0"
author: Amaury B. <amaury.bignaud@pasteur.fr>
about: Circular Contig Detection
global_settings:
- GlobalVersion
args:
- fasta_file:
short: f
long: fasta
value_name: FILE
help: Fasta with the sequences of the contigs.
takes_value: true
global: true
- out_file:
short: o
long: out-file
value_name: FILE
help: File where to write the final table output. If no value are given,
put the output in the stdout.
takes_value: true
global: true
- min_size:
short: m
long: min-size
value_name: INT
help: Minimum size to consider contigs.
takes_value: true
default_value: "0"
global: true
- threads:
short: t
long: threads
value_name: INT
help: Number of threads to use.
takes_value: true
global: true
default_value: "1"
subcommands:
- tr:
name: terminal repeat
author: Amaury B. <amaury.bignaud@pasteur.fr>
about: Search for terminal repeat in contigs sequences.
args:
- seed_size:
short: s
long: seed-size
value_name: INT
help: Seed size to use to search for terminal repeat.
takes_value: true
default_value: "20"
- sg:
name: shotgun reads
author: Amaury B. <amaury.bignaud@pasteur.fr>
about: Search for circular contigs based on shotgun reads alignment.
args:
- bam_files:
value_name: FILE
help: Alignment bam files from shotgun libraries.
takes_value: true
index: 1
multiple: true
required: true
- hic:
name: shotgun reads
author: Amaury B. <amaury.bignaud@pasteur.fr>
about: Search for circular contigs based on shotgun reads alignment.
args:
- contig_data_file:
short: c
long: contig-data
value_name: FILE
help: The contig data file have the metator output format and
needs only the 'Name' and 'Size' column. But a tabulation
separated file with two column with an header 'Name'
(contigs names from the fasta assembly) and 'Size' will
work.
takes_value: true
required: true
- cov_threshold:
short: q
long: cov_threshold
value_name: FLOAT
help: Number of HiC contacts per base pair.
takes_value: true
default_value: "0.1"
- enzyme:
short: e
long: enzyme
value_name: STR
help: The list of restriction enzyme separated by a comma used
to digest.
takes_value: true
default_value: "HpaII"
- pairs_files:
value_name: FILE
help: Alignment pairs files from hic libraries. To have a fast
run they should be index using pairix.
takes_value: true
index: 1
multiple: true
required: true
- plot:
short: p
long: plot
value_name: DIR
help: If one directrory given, plot the contact map which have
enough signal.
takes_value: true
default_value: "None"
- tmp_dir:
short: T
long: tmp-dir
value_name: DIR
help: Directory for storing intermediary files and temporary
files.
takes_value: true
default_value: "./tmp"
- all:
name: all
author: Amaury B. <amaury.bignaud@pasteur.fr>
about: Search for circular contigs based on their sequences, shotgun
reads alignment and the hic contact map.
args:
- seed_size:
short: s
long: seed-size
value_name: INT
help: Seed size to use to search for terminal repeat.
takes_value: true
default_value: "20"
- bam_files:
short: b
long: bam-files
value_name: FILE
help: Alignment bam files from shotgun libraries.
takes_value: true
multiple: true
required: true
- pairs_files:
short: P
long: pairs-files
value_name: FILE
help: Alignment pairs files from hic libraries. To have a fast
run they should be index using pairix.
takes_value: true
multiple: true
required: true
- contig_data_file:
short: c
long: contig-data
value_name: FILE
help: The contig data file have the metator output format and
needs only the 'Name' and 'Size' column. But a tabulation
separated file with two column with an header 'Name'
(contigs names from the fasta assembly) and 'Size' will
work.
takes_value: true
required: true
- enzyme:
short: e
long: enzyme
value_name: STR
help: The list of restriction enzyme separated by a comma used
to digest.
takes_value: true
default_value: "HpaII"
- plot:
short: p
long: plot
value_name: DIR
help: If one directrory given, plot the contact map which have
enough signal.
takes_value: true
default_value: "None"
- tmp_dir:
short: T
long: tmp-dir
value_name: DIR
help: Directory for storing intermediary files and temporary
files.
takes_value: true
default_value: "./tmp"
- skip_workflow:
short: w
long: skip-workflow
value_name: STR
help: Workflow to skip. Four possible values, 'tr', 'sg', 'hic'
or 'None'.
takes_value: true
default_value: "None"