[med-svn] [gubbins] 01/01: Enhance manpage

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository gubbins.

commit c9bcbcff112472de887bdbf858aee2da02a2e59d
Author: Andreas Tille <tille at debian.org>
Date:   Mon Nov 30 12:27:31 2015 +0100

    Enhance manpage
---
 debian/run_gubbins.1 | 89 ++++++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 83 insertions(+), 6 deletions(-)

diff --git a/debian/run_gubbins.1 b/debian/run_gubbins.1
index 1816ddd..0797b9d 100644
--- a/debian/run_gubbins.1
+++ b/debian/run_gubbins.1
@@ -1,10 +1,10 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
 .TH RUN_GUBBINS "1" "November 2015" "run_gubbins 1.4.3" "User Commands"
 .SH NAME
-run_gubbins \- Phylogenetic analysis of genome sequences
-.SH DESCRIPTION
-usage: run_gubbins [\-h] [\-\-outgroup OUTGROUP] [\-\-starting_tree STARTING_TREE]
-.IP
+run_gubbins \- phylogenetic analysis of genome sequences
+.SH SYNOPSIS
+.B run_gubbins
+[\-h] [\-\-outgroup OUTGROUP] [\-\-starting_tree STARTING_TREE]
 [\-\-use_time_stamp] [\-\-verbose] [\-\-no_cleanup]
 [\-\-tree_builder TREE_BUILDER] [\-\-iterations ITERATIONS]
 [\-\-min_snps MIN_SNPS]
@@ -13,7 +13,84 @@ usage: run_gubbins [\-h] [\-\-outgroup OUTGROUP] [\-\-starting_tree STARTING_TRE
 [\-\-version] [\-\-min_window_size MIN_WINDOW_SIZE]
 [\-\-max_window_size MAX_WINDOW_SIZE]
 alignment_filename
+.SH DESCRIPTION
+Gubbins supports rapid phylogenetic analysis of large samples of
+recombinant bacterial whole genome sequences.
+.P
+Gubbins (Genealogies Unbiased By recomBinations In Nucleotide
+Sequences) is an algorithm that iteratively identifies loci containing
+elevated densities of base substitutions while concurrently constructing
+a phylogeny based on the putative point mutations outside of these
+regions. Simulations demonstrate the algorithm generates highly accurate
+reconstructions under realistic models of short-term bacterial
+evolution, and can be run in only a few hours on alignments of hundreds
+of bacterial genome sequences.
+.SH OPTIONS
+.SS "positional arguments:"
+.TP
+alignment_filename
+Multifasta alignment file
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-outgroup\fR OUTGROUP, \fB\-o\fR OUTGROUP
+Outgroup name for rerooting. A list of comma separated
+names can be used if they form a clade
+.TP
+\fB\-\-starting_tree\fR STARTING_TREE, \fB\-s\fR STARTING_TREE
+Starting tree
+.TP
+\fB\-\-use_time_stamp\fR, \fB\-u\fR
+Use a time stamp in file names
+.TP
+\fB\-\-verbose\fR, \fB\-v\fR
+Turn on debugging
+.TP
+\fB\-\-no_cleanup\fR, \fB\-n\fR
+Dont cleanup intermediate files
+.TP
+\fB\-\-tree_builder\fR TREE_BUILDER, \fB\-t\fR TREE_BUILDER
+Application to use for tree building
+[raxml|fasttree|hybrid], default RAxML
+.TP
+\fB\-\-iterations\fR ITERATIONS, \fB\-i\fR ITERATIONS
+Maximum No. of iterations, default is 5
+.TP
+\fB\-\-min_snps\fR MIN_SNPS, \fB\-m\fR MIN_SNPS
+Min SNPs to identify a recombination block, default is
+3
+.TP
+\fB\-\-filter_percentage\fR FILTER_PERCENTAGE, \fB\-f\fR FILTER_PERCENTAGE
+Filter out taxa with more than this percentage of
+gaps, default is 25
+.TP
+\fB\-\-prefix\fR PREFIX, \fB\-p\fR PREFIX
+Add a prefix to the final output filenames
+.TP
+\fB\-\-threads\fR THREADS, \fB\-c\fR THREADS
+Number of threads to run with RAXML, but only if a
+PTHREADS version is available
+.TP
+\fB\-\-converge_method\fR CONVERGE_METHOD, \fB\-z\fR CONVERGE_METHOD
+Criteria to use to know when to halt iterations [weigh
+ted_robinson_foulds|robinson_foulds|recombination]
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-min_window_size\fR MIN_WINDOW_SIZE, \fB\-a\fR MIN_WINDOW_SIZE
+Minimum window size, default 100
+.TP
+\fB\-\-max_window_size\fR MAX_WINDOW_SIZE, \fB\-b\fR MAX_WINDOW_SIZE
+Maximum window size, default 10000
+.SH SEE ALSO
 .PP
-run_gubbins: error: the following arguments are required: alignment_filename
+Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley
+S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples
+of recombinant bacterial whole genome sequences using Gubbins". Nucleic Acids
+Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196.
 .SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+This manpage was written by Andreas Tille for the Debian distribution and can
+be used for any other usage of the program.

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