The usage and help documentation of can be seen by running -h:

usage: - [-h] [--samplenames SAMPLENAMES] bedfile bamfiles [bamfiles ...]

A script to generate the input coverage table for CONCOCT using a BEDFile.
Output is written to stdout. The BEDFile defines the regions used as
subcontigs for concoct. This makes it possible to get the coverage for
subcontigs without specifically mapping reads against the subcontigs. @author:
inodb, alneberg

positional arguments:
  bedfile               Contigs BEDFile with four columns representing:
                        'Contig ID, Start Position, End Position and SubContig
                        ID' respectively. The Subcontig ID must contain the
                        pattern 'concoct_part_[0-9]*' while the contigs which
                        are not cutup cannot contain this pattern. This file
                        can be generated by the script.
  bamfiles              BAM files with mappings to the original contigs.

optional arguments:
  -h, --help            show this help message and exit
  --samplenames SAMPLENAMES
                        File with sample names, one line each. Should be same
                        nr of bamfiles. Default sample names used are the file
                        names of the bamfiles, excluding the file extension.


An example of how to run contigs_10K.bed mapping/Sample*.sorted.bam > coverage_table.tsv

This creates a coverage table suitable as input for concoct as the coverage_file parameter. The contigs_10K.bed file is created from the script and the bam-files needs to be sorted and indexed.