Add autogenerated manpages (b58f9042) · Commits · Debian Med / kma

debian/createmanpages

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		#!/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: *//'`
		PROGNAME=`grep "^Package:" debian/control \| head -n1 \| sed 's/^Package: *//'`

		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
		for progname in kma kma_index kma_shm ; do
		NAME=`${progname} -h \| head -n1 \| sed -e 's/^# \+[^ ]\+ \+//' -e 's/\. *$//'`

		echo "#!/bin/sh" > /tmp/${progname}
		echo "cat <<EOT" >> /tmp/${progname}
		/usr/bin/${progname} -h \| sed 's/^#//' >> /tmp/${progname}
		echo "EOT" >> /tmp/${progname}
		chmod +x /tmp/${progname}
		help2man --no-info --no-discard-stderr --help-option=" " \
		--name="$NAME" \
		--version-string="$VERSION" /tmp/${progname} > $MANDIR/${progname}.1
		echo $AUTHOR >> $MANDIR/${progname}.1
		done

		cat <<EOT
		Please enhance the help2man output.
		The following web page might be helpful in doing so:
		http://liw.fi/manpages/
		EOT

debian/kma.1

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		.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
		.TH KMA "1" "June 2018" "kma 0.14.4+git20180611.7e14ef6" "User Commands"
		.SH NAME
		kma \- mapps raw reads to a template database, for optimal performance it is designed to use 3 threads
		.SH DESCRIPTION
		.IP
		KMA\-0.14.4 mapps raw reads to a template database, for optimal performance it is designed to use 3 threads.
		Options are: Desc: Default: Requirements:
		.TP
		\fB\-o\fR
		Output file None REQUIRED
		.TP
		\fB\-t_db\fR
		Template DB None REQUIRED
		.TP
		\fB\-i\fR
		Input file name(s) STDIN
		.TP
		\fB\-ipe\fR
		Input paired end file name(s)
		.TP
		\fB\-int\fR
		Input interleaved file name(s)
		.TP
		\fB\-k\fR
		Kmersize DB defined
		.TP
		\fB\-e\fR
		evalue 0.05
		.TP
		\fB\-mem_mode\fR
		Use kmers to choose best
		template, and save memory False
		.TP
		\fB\-ex_mode\fR
		Searh kmers exhaustively False
		.TP
		\fB\-deCon\fR
		Remove contamination False
		.TP
		\fB\-dense\fR
		Do not allow insertions
		in assembly False
		.TP
		\fB\-ref_fsa\fR
		Consensus sequnce will
		have "n" instead of gaps False
		.TP
		\fB\-matrix\fR
		Print assembly matrix False
		.TP
		\fB\-a\fR
		Print all best mappings False
		.TP
		\fB\-mp\fR
		Minimum phred score 30
		.TP
		\fB\-5p\fR
		Cut a constant number of
		nucleotides from the 5 prime. 0
		.TP
		\fB\-Sparse\fR
		Only count kmers False
		.TP
		\fB\-Mt1\fR
		Map only to "num" template. 0 / False
		.TP
		\fB\-ID\fR
		Minimum ID 1.0%
		.TP
		\fB\-ss\fR
		Sparse sorting (q,c,d) q
		.TP
		\fB\-pm\fR
		Pairing method (p,u,f) u
		.TP
		\fB\-fpm\fR
		Fine Pairing method (p,u,f) u
		.TP
		\fB\-apm\fR
		Sets both pm and fpm u
		.TP
		\fB\-shm\fR
		Use shared DB made by kma_shm 0 (lvl)
		.TP
		\fB\-swap\fR
		Swap DB to disk 0 (lvl)
		.TP
		\fB\-1t1\fR
		Skip HMM False
		.TP
		\fB\-boot\fR
		Bootstrap sequence False
		.TP
		\fB\-bc\fR
		Base calls should be
		significantly overrepresented. True
		.TP
		\fB\-bc90\fR
		Base calls should be both
		significantly overrepresented,
		and have 90% agreement. False
		.TP
		\fB\-bcNano\fR
		Call bases at suspicious
		deletions, made for nanopore. False
		.TP
		\fB\-and\fR
		Both mrs and p_value thresholds
		has to reached to in order to
		report a template hit. or
		.TP
		\fB\-mrs\fR
		Minimum alignment score,
		normalized to alignment length 0.50
		.TP
		\fB\-reward\fR
		Score for match 1
		.TP
		\fB\-penalty\fR
		Penalty for mismatch \fB\-2\fR
		.TP
		\fB\-gapopen\fR
		Penalty for gap opening \fB\-3\fR
		.TP
		\fB\-gapextend\fR
		Penalty for gap extension \fB\-1\fR
		.TP
		\fB\-per\fR
		Reward for pairing reads 7
		.TP
		\fB\-t\fR
		Number of threads 1
		.TP
		\fB\-v\fR
		Version
		.TP
		\fB\-h\fR
		Shows this help message
		.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/kma_index.1

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		.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
		.TH KMA_INDEX "1" "June 2018" "kma_index 0.14.4+git20180611.7e14ef6" "User Commands"
		.SH NAME
		kma_index \- creates the databases needed to run KMA, from a list of fasta files given
		.SH DESCRIPTION
		.IP
		kma_index creates the databases needed to run KMA, from a list of fasta files given.
		Options are: Desc: Default:
		.TP
		\fB\-i\fR
		Input/query file name (STDIN: "\-\-") None
		.TP
		\fB\-o\fR
		Output file Input/template file
		.TP
		\fB\-batch\fR
		Batch input file
		.TP
		\fB\-deCon\fR
		File with contamination (STDIN: "\-\-") None/False
		.TP
		\fB\-batchD\fR
		Batch decon file
		.TP
		\fB\-t_db\fR
		Add to existing DB None/False
		.TP
		\fB\-k\fR
		Kmersize 16
		.TP
		\fB\-k_t\fR
		Kmersize for template identification 16
		.TP
		\fB\-k_i\fR
		Kmersize for indexing 16
		.TP
		\fB\-ML\fR
		Minimum length of templates kmersize (16)
		.TP
		\fB\-CS\fR
		Start Chain size 1 M
		.TP
		\fB\-ME\fR
		Mega DB False
		.TP
		\fB\-Sparse\fR
		Make Sparse DB ('\-' for no prefix) None/False
		.TP
		\fB\-ht\fR
		Homology template 1.0
		.TP
		\fB\-hq\fR
		Homology query 1.0
		.TP
		\fB\-and\fR
		Both homolgy thresholds
		has to be reached or
		.TP
		\fB\-h\fR
		Shows this help message
		.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/kma_shm.1

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		.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
		.TH KMA_SHM "1" "June 2018" "kma_shm 0.14.4+git20180611.7e14ef6" "User Commands"
		.SH NAME
		kma_shm \- sets up a shared database (sysV) for mapping with KMA
		.SH DESCRIPTION
		.IP
		kma_shm sets up a shared database (sysV) for mapping with KMA.
		Options are: Desc: Default: Requirements:
		.TP
		\fB\-t_db\fR
		Template DB None REQUIRED
		.TP
		\fB\-destroy\fR
		Destroy shared DB False
		.TP
		\fB\-shmLvl\fR
		Level of shared memory 1
		.TP
		\fB\-shm\-h\fR
		Explain shm levels
		.TP
		\fB\-h\fR
		Shows this help message
		.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

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		debian/*.1