.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH IDSEQ-BENCH-SCORE "1" "July 2020" "idseq-bench-score 0.0~git20200627.4040457" "User Commands"
.SH NAME
idseq-bench-score \- Score benchmark samples based on answer key
.SH SYNOPSIS
.B idseq\-bench\-score
[\-h] [\-o OUTPUT_FILE]
[\-t [TRUTH_FILES [TRUTH_FILES ...]]] [\-e ENV]
[\-p LOCAL_PATH] [\-\-mono\-aupr]
project_id sample_id pipeline_version
.SH DESCRIPTION
Score benchmark samples based on answer key (against key encode in fastq read
IDs for IDseq Bench samples or against a provided answer key).
.SH OPTIONS
.SS "positional arguments:"
.TP
project_id
ID of the project
.TP
sample_id
ID of the sample
.TP
pipeline_version
Pipeline version to retrieve: <major>.<minor>
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR OUTPUT_FILE, \fB\-\-output\-file\fR OUTPUT_FILE
Path of output file to write the results to (if not
set results are written to stdout)
.TP
\fB\-t\fR [TRUTH_FILES [TRUTH_FILES ...]], \fB\-\-truth_files\fR [TRUTH_FILES [TRUTH_FILES ...]]
Space separated list of truth files. Truth files are
TSV files with the fields <tax_id, absolute abundance,
relative abundance, rank, tax_name>
.TP
\fB\-e\fR ENV, \fB\-\-env\fR ENV
String name of environment in which sample exists;
options are: prod (default), staging
.TP
\fB\-p\fR LOCAL_PATH, \fB\-\-local\-path\fR LOCAL_PATH
Root of local path where IDseq files are stored. Must
follow the same structure to store files as IDseq
.TP
\fB\-\-mono\-aupr\fR
Computed adjusted AUPR by forcing the precision/recall
curve to be monotonic decreasing
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.