debian/createmanpages

+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT

debian/kleborate.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
+.TH KLEBORATE "1" "September 2019" "kleborate 0.3.0" "User Commands"
+.SH NAME
+kleborate \- tool to screen Klebsiella genome assemblies
+.SH SYNOPSIS
+.B kleborate
+\fB\-a\fR ASSEMBLIES [ASSEMBLIES ...] [\-r] [\-s] [\-\-kaptive_k]
+[\-\-kaptive_o] [\-k] [\-\-all] [\-o OUTFILE]
+[\-\-kaptive_k_outfile KAPTIVE_K_OUTFILE]
+[\-\-kaptive_o_outfile KAPTIVE_O_OUTFILE] [\-h] [\-\-version]
+.SH DESCRIPTION
+Kleborate: a tool for characterising virulence and resistance in Klebsiella
+.SH OPTIONS
+.SS "Required arguments:"
+.TP
+\fB\-a\fR ASSEMBLIES [ASSEMBLIES ...], \fB\-\-assemblies\fR ASSEMBLIES [ASSEMBLIES ...]
+FASTA file(s) for assemblies
+.SS "Screening options:"
+.TP
+\fB\-r\fR, \fB\-\-resistance\fR
+Turn on resistance genes screening (default: no
+resistance gene screening)
+.TP
+\fB\-s\fR, \fB\-\-species\fR
+Turn on Klebsiella species identification (requires
+Mash, default: no species identification)
+.TP
+\fB\-\-kaptive_k\fR
+Turn on Kaptive screening of K loci (default: do not
+run Kaptive for K loci)
+.TP
+\fB\-\-kaptive_o\fR
+Turn on Kaptive screening of O loci (default: do not
+run Kaptive for O loci)
+.TP
+\fB\-k\fR, \fB\-\-kaptive\fR
+Equivalent to \fB\-\-kaptive_k\fR \fB\-\-kaptive_o\fR
+.TP
+\fB\-\-all\fR
+Equivalent to \fB\-\-resistance\fR \fB\-\-species\fR \fB\-\-kaptive\fR
+.SS "Output options:"
+.TP
+\fB\-o\fR OUTFILE, \fB\-\-outfile\fR OUTFILE
+File for detailed output (default:
+Kleborate_results.txt)
+.TP
+\fB\-\-kaptive_k_outfile\fR KAPTIVE_K_OUTFILE
+File for full Kaptive K locus output (default: do not
+save Kaptive K locus results to separate file)
+.TP
+\fB\-\-kaptive_o_outfile\fR KAPTIVE_O_OUTFILE
+File for full Kaptive O locus output (default: do not
+save Kaptive O locus results to separate file)
+.SS "Help:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Show this help message and exit
+.TP
+\fB\-\-version\fR
+Show program's version number and exit
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/manpages

+debian/*.1

debian/tests/control_readme

+Upstream provided a script test.sh which unfortunately does not work:
+
+$ kleborate -p . -o details.txt *.fna
+usage: kleborate -a ASSEMBLIES [ASSEMBLIES ...] [-r] [-s] [--kaptive_k]
+                 [--kaptive_o] [-k] [--all] [-o OUTFILE]
+                 [--kaptive_k_outfile KAPTIVE_K_OUTFILE]
+                 [--kaptive_o_outfile KAPTIVE_O_OUTFILE] [-h] [--version]
+kleborate: error: the following arguments are required: -a/--assemblies

debian/tests/data/get-data

+## Adopted from test.sh script to just obtain the data
+#
+# NTUH-K2044 (ST23, ybt 2; ICEKp1)
+wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/009/885/GCA_000009885.1_ASM988v1/GCA_000009885.1_ASM988v1_genomic.fna.gz
+gunzip GCA_000009885.1_ASM988v1_genomic.fna.gz
+mv GCA_000009885.1_ASM988v1_genomic.fna NTUH-K2044.fna
+
+# Kp1084 (ST23, ybt 1; ICEKp10, clb 2)
+wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/294/365/GCA_000294365.1_ASM29436v1/GCA_000294365.1_ASM29436v1_genomic.fna.gz
+gunzip GCA_000294365.1_ASM29436v1_genomic.fna.gz
+mv GCA_000294365.1_ASM29436v1_genomic.fna Klebs_Kp1084.fna
+
+# HS11286 (ST11, ybt 9; ICEKp3)
+wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/240/185/GCA_000240185.2_ASM24018v2/GCA_000240185.2_ASM24018v2_genomic.fna.gz
+gunzip GCA_000240185.2_ASM24018v2_genomic.fna.gz
+mv GCA_000240185.2_ASM24018v2_genomic.fna Klebs_HS11286.fna
+
+# MGH 78578 (ST38, no ICE)
+wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/016/305/GCA_000016305.1_ASM1630v1/GCA_000016305.1_ASM1630v1_genomic.fna.gz
+gunzip GCA_000016305.1_ASM1630v1_genomic.fna.gz
+mv GCA_000016305.1_ASM1630v1_genomic.fna MGH78578.fna
+
+xz *.fna