[med-svn] [velvetoptimiser] 05/11: Add help2man based manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository velvetoptimiser.

commit ca7790da3aaef1dbab3bc0e430f47004f1b8699f
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 30 11:02:03 2014 +0000

    Add help2man based manpage
---
 debian/manpages          |  1 +
 debian/velvetoptimiser.1 | 77 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 78 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/velvetoptimiser.1 b/debian/velvetoptimiser.1
new file mode 100644
index 0000000..53be6a5
--- /dev/null
+++ b/debian/velvetoptimiser.1
@@ -0,0 +1,77 @@
+.TH VELVETOPTIMISER "1" "June 2014" "velvetoptimiser 2.2.5" "User Commands"
+.SH NAME
+velvetoptimiser \- Automatically optimise Velvet do novo assembly parameters
+.SH SYNOPSIS
+.B velvetoptimiser
+[\fI\,options\/\fR] \fI\,-f 'velveth input line'\/\fR
+.SH DESCRIPTION
+VelvetOptimiser is a multi-threaded Perl script for automatically optimising
+the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet
+de novo sequence assembler.
+.SH OPTIONS
+.TP
+\fB\-\-help\fR
+This help.
+.TP
+\fB\-\-version\fR!
+Print version to stdout and exit. (default '0').
+.TP
+\fB\-\-v\fR|verbose+
+Verbose logging, includes all velvet output in the logfile. (default '0').
+.TP
+\fB\-\-s\fR|hashs=i
+The starting (lower) hash value (default '19').
+.TP
+\fB\-\-e\fR|hashe=i
+The end (higher) hash value (default '31').
+.TP
+\fB\-\-x\fR|step=i
+The step in hash search..  min 2, no odd numbers (default '2').
+.HP
+\fB\-\-f\fR|velvethfiles=s The file section of the velveth command line. (default '0').
+.TP
+\fB\-\-a\fR|amosfile!
+Turn on velvet's read tracking and amos file output. (default '0').
+.TP
+\fB\-\-o\fR|velvetgoptions=s Extra velvetg options to pass through.
+eg. \fB\-long_mult_cutoff\fR \fB\-max_coverage\fR etc (default '').
+.TP
+\fB\-\-t\fR|threads=i
+The maximum number of simulataneous velvet instances to run. (default '4').
+.TP
+\fB\-\-g\fR|genomesize=f The approximate size of the genome to be assembled in megabases.
+Only used in memory use estimation. If not specified, memory use estimation
+will not occur. If memory use is estimated, the results are shown and then program exits. (default '0').
+.HP
+\fB\-\-k\fR|optFuncKmer=s The optimisation function used for k\-mer choice. (default 'n50').
+.HP
+\fB\-\-c\fR|optFuncCov=s The optimisation function used for cov_cutoff optimisation. (default 'Lbp').
+.HP
+\fB\-\-m\fR|minCovCutoff=f The minimum cov_cutoff to be used. (default '0').
+.TP
+\fB\-\-p\fR|prefix=s
+The prefix for the output filenames, the default is the date and time in the format DD\-MM\-YYYY\-HH\-MM_. (default 'auto').
+.HP
+\fB\-\-d\fR|dir_final=s The name of the directory to put the final output into. (default '.').
+.HP
+\fB\-\-z\fR|upperCovCutoff=f The maximum coverage cutoff to consider as a multiplier of the expected coverage. (default '0.8').
+.PP
+Advanced!: Changing the optimisation function(s)
+.PP
+Velvet optimiser assembly optimisation function can be built from the following variables.
+.IP
+LNbp = The total number of Ns in large contigs
+Lbp = The total number of base pairs in large contigs
+Lcon = The number of large contigs
+max = The length of the longest contig
+n50 = The n50
+ncon = The total number of contigs
+tbp = The total number of basepairs in contigs
+.SS "Examples are:"
+.IP
+\&'Lbp' = Just the total basepairs in contigs longer than 1kb
+\&'n50*Lcon' = The n50 times the number of long contigs.
+\&'n50*Lcon/tbp+log(Lbp)' = The n50 times the number of long contigs divided
+.IP
+by the total bases in all contigs plus the log of the number of bases
+in long contigs.

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