[med-svn] [clonalorigin] 01/01: Add manpages
Andreas Tille
tille at debian.org
Sun Dec 3 14:41:26 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository clonalorigin.
commit f627fc85e894a8b0f24d43b159066e21c3d7262f
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 3 14:36:35 2017 +0100
Add manpages
---
debian/clonalorigin-gui.1 | 123 +++++++++++++++++++++++++++++++++++++++
debian/clonalorigin-gui.manpages | 1 +
debian/clonalorigin.1 | 2 +
debian/clonalorigin.manpages | 1 +
debian/createmanpages | 28 +++++++++
debian/warg.1 | 122 ++++++++++++++++++++++++++++++++++++++
6 files changed, 277 insertions(+)
diff --git a/debian/clonalorigin-gui.1 b/debian/clonalorigin-gui.1
new file mode 100644
index 0000000..266ed25
--- /dev/null
+++ b/debian/clonalorigin-gui.1
@@ -0,0 +1,123 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH CLONALORIGIN-GUI "1" "December 2017" "clonalorigin-gui 1.0" "User Commands"
+.SH NAME
+clonalorigin-gui \- GUI for clonalorigin
+.SH Synopsis
+.B clonalorigin-gui
+[OPTIONS] <filename>
+.SH DESCRIPTION
+For graphical use, no options are necessary.
+To pre\-run a limited set of functions, or use batch
+mode, the following options can be used.
+NOTE: They are processed IN ORDER, so be sure to open
+the file before using it, and set output names before
+producing the output!
+.SH OPTIONS
+.TP
+\fB\-b\fR Batch mode. Perform operations then quit
+.IP
+without displaying the gui.
+.TP
+\fB\-o\fR <filename>
+Open the specified input XML file.
+.TP
+\fB\-c\fR <filename><:num>
+Write a csv file of the main features. If
+:num is provided then it changes the variables
+in the output (default 2):
+.IP
+:1 \- Parameters only
+.IP
+:2 \- Parameters + Number of recedges
+.IP
+:3 \- Parameters + Clonal Pairwise Distances
+.IP
+:4 \- All of the above.
+.TP
+\fB\-T\fR <filename>
+Redirect the batch processed output
+from stdout to the file specified.
+Specify to display to the gui.
+.TP
+\fB\-t\fR <list>
+Perform a convergence of trees test
+between the open file and the set of
+specified files (separated by commas).
+.TP
+\fB\-g\fR <list><:num> Perform a gelman\-rubin test
+between the open file and the set of
+specified files (separated by commas).
+<num> takes the same meaning as for \fB\-c\fR.
+.TP
+\fB\-S\fR <filename>
+Redirect the Score against true tree output
+from stdout to the file specified.
+Specify to display to the gui.
+.TP
+\fB\-s\fR <filename>
+Perform a score against true tree test
+against the newick\-format file specified.
+.TP
+\fB\-C\fR <i>
+Performs a consensus\-of\-trees either with
+the specified cutoff (integer i=0\-100) or
+an extended consensus if i<0.
+.TP
+\fB\-H\fR 0/1/2/3
+Extract the heatmap. Pass 0 for no prior correction,
+1 for correction in number of std, 2 for correction
+measured in proportion or 3 for prior only.
+.TP
+\fB\-d\fR 0/1/2/3
+Extract the pairwise clonal tree heatmap. Pass 0 for
+no prior correction,
+1 for correction in number of std, 2 for correction
+measured in proportion or 3 for prior only.
+.TP
+\fB\-e\fR <operation>:<value>:<filename>
+Extract iterations and thin. <operation> is either
+either "thin" with value "x" to thin every
+x'th iteration, or "extract" with value "x\-y" to extract
+iterations between x and y. The outputfile is after
+the final colon.
+.TP
+\fB\-E\fR <filenames>:<filename>
+Combines the list of output files specified NOT
+including the current one, separated by commas, and
+outputs to the file after the colon.
+.TP
+\fB\-n\fR
+Start in the display mode without recombination (You must
+specify the outputfile with \fB\-o\fR).
+.TP
+\fB\-h\fR
+This help message.
+.PP
+
+.SH EXAMPLES
+.HP
+\fB\-o\fR test1.xml \fB\-t\fR test2.xml \fB\-b\fR:
+.IP
+Performs a convergence of tree test between files
+test1.xml and test2.xml, printing the results to
+stdout and exiting the program.
+.HP
+\fB\-o\fR test1.xml \fB\-t\fR test2.xml:
+.IP
+As above, but leave the gui window open.
+.HP
+\fB\-o\fR test1.xml \fB\-T\fR \fB\-t\fR test2.xml:
+.IP
+As above, but opens the results in the gui
+and with the gui window open.
+.HP
+\fB\-o\fR test1.xml \fB\-t\fR test2.xml,test3.xml \fB\-b\fR:
+.IP
+Performs a convergence of tree test between files
+test1.xml, test2.xml and test3.xml.
+.HP
+\fB\-t\fR test1.xml \fB\-o\fR test2.xml \fB\-b\fR:
+.IP
+Fails.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/clonalorigin-gui.manpages b/debian/clonalorigin-gui.manpages
new file mode 100644
index 0000000..3af3921
--- /dev/null
+++ b/debian/clonalorigin-gui.manpages
@@ -0,0 +1 @@
+debian/clonalorigin-gui.1
diff --git a/debian/clonalorigin.1 b/debian/clonalorigin.1
new file mode 100644
index 0000000..e1ebf19
--- /dev/null
+++ b/debian/clonalorigin.1
@@ -0,0 +1,2 @@
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/clonalorigin.manpages b/debian/clonalorigin.manpages
new file mode 100644
index 0000000..206fea4
--- /dev/null
+++ b/debian/clonalorigin.manpages
@@ -0,0 +1 @@
+debian/warg.1
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..74d737d
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=clonalorigin-gui
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='GUI for clonalorigin' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=warg
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name='inference of homologous recombination in bacteria using whole genome sequences' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/warg.1 b/debian/warg.1
new file mode 100644
index 0000000..465cc84
--- /dev/null
+++ b/debian/warg.1
@@ -0,0 +1,122 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.5.
+.TH WARG "1" "December 2017" "warg 1.0" "User Commands"
+.SH NAME
+warg \- inference of homologous recombination in bacteria using whole genome sequences
+.SH SYNOPSIS
+.B warg
+[OPTIONS] treefile datafile outputfile
+.SH DESCRIPTION
+ Bacteria, unlike us, can reproduce on their own. They do however have
+ mechanisms that transfer DNA between organisms, a process more formally
+ known as recombination. The mechanisms by which recombination takes
+ place have been studied extensively in the laboratory but much remains
+ to be understood concerning how, when and where recombination takes
+ place within natural populations of bacteria and how it helps them to
+ adapt to new environments. ClonalOrigin performs a comparative analysis
+ of the sequences of a sample of bacterial genomes in order to
+ reconstruct the recombination events that have taken place in their
+ ancestry.
+.SH OPTIONS
+.TP
+\fB\-w\fR NUM
+Sets the number of pre burn\-in iterations (default is 100000)
+.TP
+\fB\-x\fR NUM
+Sets the number of burn\-in iterations (default is 100000)
+.TP
+\fB\-y\fR NUM
+Sets the number of iterations after burn\-in (default is 100000)
+.TP
+\fB\-z\fR NUM
+Sets the number of iterations between samples (default is 100)
+.TP
+\fB\-T\fR NUM
+Sets the value of theta. Use sNUM instead of NUM for per\-site
+.TP
+\fB\-R\fR NUM
+Sets the value of rho. Use sNUM instead of NUM for per\-site
+.TP
+\fB\-D\fR NUM
+Sets the value of delta
+.TP
+\fB\-s\fR NUM
+Use given seed to initiate random number generator
+.TP
+\fB\-S\fR NUM,SEED
+Run on a subset of NUM regions determined by seed SEED
+.IP
+NUM/NUM/../NUM
+Run on a specified region(s) given by each NUM.
+.TP
+\fB\-r\fR NUM
+Perform r tempered steps between topological updates (default:0)
+.TP
+\fB\-t\fR NUM
+Tempered at "temperature" t for topological updates (default:1.0)
+.TP
+\fB\-U\fR
+Start from UPGMA tree, rather than the default random tree.
+.TP
+\fB\-G\fR NUM
+Greedily compute the "best fit" tree, given the recombination
+observed on the current tree. If NUM is negative and a previous
+run is provided, the tree is calculated from all observed values.
+If NUM is positive, a "greedy move" is performed with weight
+NUM (see \fB\-a\fR). Note that this is NOT an MCMC move and causes bias.
+.TP
+\fB\-a\fR NUM,...,NUM
+Set the ELEVEN (real valued) move weightings to the given vector,
+with weightings separated by commas (NOT SPACES).
+The weightings need not sum to 1, but must be in the following order:
+.IP
+MoveRho (ignored if not needed)
+.IP
+MoveDelta (ignored if not needed)
+.IP
+MoveTheta (ignored if not needed)
+.IP
+MoveRemEdge
+.IP
+MoveAddEdge
+.IP
+MoveSiteChange
+.IP
+MoveTimeChange
+.IP
+MoveEdgeChange
+.IP
+MoveAgeClonal
+.IP
+MoveScaleTree
+.IP
+MoveRegraftClonal
+.TP
+\fB\-i\fR NUM,...,NUM
+Set the SIX parameters for creating random Recombination Trees
+under the inference model. The parameters are:
+.IP
+N (integer) The number of sequences in the sample (default 10)
+.IP
+n_B (integer) The number of block boundaries in the sample (default 8)
+.IP
+l_B (integer) The length of each block: L=n_B * l_B (default 500)
+.IP
+delta (real) The average length of imports (default 500.0)
+.IP
+theta (real) The mutation rate NOT per site (default 100.0)
+.IP
+rho (real) The recombination rate NOT per site (default 50.0)
+.TP
+\fB\-f\fR
+Forbid topology changes, (allowing updates of coalescence times).
+.TP
+\fB\-v\fR
+Verbose mode
+.TP
+\fB\-h\fR
+This help message
+.TP
+\fB\-V\fR
+Print Version info
+.SH AUTHOR
+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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