[med-svn] [roguenarok] 02/02: Manual edits of manpages
Andreas Tille
tille at debian.org
Tue Mar 14 11:01:24 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository roguenarok.
commit cc19c6fa7911d0601ac8b1a1bae450807a04ecb0
Author: Andreas Tille <tille at debian.org>
Date: Tue Mar 14 11:53:34 2017 +0100
Manual edits of manpages
---
debian/createmanpages | 12 +++----
debian/manpages | 1 +
debian/mans/rnr-lsi.1 | 34 +++++++-------------
debian/mans/rnr-mast.1 | 37 +++++++--------------
debian/mans/rnr-prune.1 | 35 +++++++-------------
debian/mans/rnr-tii.1 | 35 +++++++-------------
debian/mans/roguenarok-parallel.1 | 67 +++++++++++++++------------------------
debian/mans/roguenarok-single.1 | 64 +++++++++++++------------------------
8 files changed, 101 insertions(+), 184 deletions(-)
diff --git a/debian/createmanpages b/debian/createmanpages
index f1dff8c..3d82bcf 100755
--- a/debian/createmanpages
+++ b/debian/createmanpages
@@ -10,36 +10,36 @@ can be used for any other usage of the program.
progname=roguenarok-parallel
help2man --no-info --no-discard-stderr --help-option=" --help" \
- --name='computes the taxonomic instability index (parallel version)' \
+ --name='implements the RogueNaRok algorithm for rogue taxon identification (parallel version)' \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
progname=roguenarok-single
help2man --no-info --no-discard-stderr --help-option=" " \
- --name='computes the taxonomic instability index (single core version)' \
+ --name='implements the RogueNaRok algorithm for rogue taxon identification (single core version)' \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
progname=rnr-lsi
-help2man --no-info --no-discard-stderr --help-option=" " \
+help2man --no-info --no-discard-stderr --help-option=" -h" \
--name='computes three flavors of leaf stability index for each taxon' \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
progname=rnr-mast
-help2man --no-info --no-discard-stderr --help-option=" " \
+help2man --no-info --no-discard-stderr --help-option=" -h" \
--name='computes maximum agreement trees for unrooted input sets' \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
progname=rnr-prune
-help2man --no-info --no-discard-stderr --help-option=" " \
+help2man --no-info --no-discard-stderr --help-option=" -h" \
--name='prunes a list of taxa from a bootstrap tree or a single tree with branch lengths' \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
progname=rnr-tii
-help2man --no-info --no-discard-stderr --help-option=" " \
+help2man --no-info --no-discard-stderr --help-option=" -h" \
--name='computes the taxonomic instability index' \
--version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
echo $AUTHOR >> $MANDIR/${progname}.1
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/rnr-lsi.1 b/debian/mans/rnr-lsi.1
index 511ddb1..603e36e 100644
--- a/debian/mans/rnr-lsi.1
+++ b/debian/mans/rnr-lsi.1
@@ -1,38 +1,26 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH RNR-LSI "1" "March 2017" "rnr-lsi 1.0" "User Commands"
.SH NAME
rnr-lsi \- computes three flavors of leaf stability index for each taxon
-.SH DESCRIPTION
-Please specify a file containing bootstrap trees via \fB\-i\fR.
-.PP
-This is RnR\-lsi version 1.0 released by Andre J. Aberer in 2011\-10\-25.
-.PP
-This program computes three flavors of leaf stability index for each taxon.
-.PP
-SYNTAX: ./rnr\-lsi \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
-.IP
-OBLIGATORY:
-.PP
+.SH SYNOPSIS
+.B rnr\-lsi
+\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
+.SH OPTIONS
+.SS OBLIGATORY
+.TP
\fB\-i\fR <bootTrees>
-.IP
A collection of bootstrap trees.
-.PP
+.TP
\fB\-n\fR <runId>
-.IP
An identifier for this run.
-.IP
-OPTIONAL:
-.PP
+.SS OPTIONAL
+.TP
\fB\-x\fR <excludeFile>
-.IP
Prune the taxa in the file first (one taxon per line), before computing the lsi.
-.PP
+.TP
\fB\-w\fR <workDir>
-.IP
A working directory where output files are created.
-.PP
+.TP
\fB\-h\fR
-.IP
This help file.
.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/mans/rnr-mast.1 b/debian/mans/rnr-mast.1
index cb88bc6..6b9cfe4 100644
--- a/debian/mans/rnr-mast.1
+++ b/debian/mans/rnr-mast.1
@@ -1,47 +1,34 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH RNR-MAST "1" "March 2017" "rnr-mast 1.0" "User Commands"
.SH NAME
rnr-mast \- computes maximum agreement trees for unrooted input sets
-.SH DESCRIPTION
-Please specify a file containing bootstrap trees via \fB\-i\fR.
-.PP
-This is RnR\-mast version 1.0 released by Andre J. Aberer in 2011\-10\-25.
-.PP
-This program computes maximum agreement trees for unrooted input sets.
-.PP
-SYNTAX: ./rnr\-mast \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-a] [\-x <excludeFile>]
-.PP
-OBLIGATORY:
+.SH SYNOPSIS
+.B rnr\-mast
+\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-a] [\-x <excludeFile>]
+.SH OPTIONS
+.SS OBLIGATORY
+.TP
\fB\-i\fR <bootTrees>
-.IP
A collection of bootstrap trees.
-.PP
+.TP
\fB\-n\fR <runId>
-.IP
An identifier for this run.
-.PP
-OPTIONAL
+.SS OPTIONAL
+.TP
\fB\-a\fR
-.IP
Compute all possible MAST trees. Without this flag, you will
-.IP
only get a few MASTs that are easy to compute. As there may be an
exponential number of MASTs, use this option with care.
-.PP
+.TP
\fB\-w\fR <workDir>
-.IP
A working directory where output files are created.
-.PP
+.TP
\fB\-x\fR <excludeFile>
-.IP
Exclude the taxa in this file (one taxon per line)
-.IP
prior to computing the MAST. If you compute all MASTs anyway, this
option is option will not be useful. However, you can use this option
to speed up things.
-.PP
+.TP
\fB\-h\fR
-.IP
This help file.
.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/mans/rnr-prune.1 b/debian/mans/rnr-prune.1
index 7562b2d..40ca214 100644
--- a/debian/mans/rnr-prune.1
+++ b/debian/mans/rnr-prune.1
@@ -1,42 +1,31 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH RNR-PRUNE "1" "March 2017" "rnr-prune 1.0" "User Commands"
.SH NAME
rnr-prune \- prunes a list of taxa from a bootstrap tree or a single tree with branch lengths
+.SH SYNOPSIS
+.B rnr\-prune
+[\-i <bootTrees> | \fB\-t\fR <treeFile>] \fB\-x\fR <excludeFile> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
.SH DESCRIPTION
-Please specify either a set of bootstrap trees (\fB\-i\fR) or a single best\-known tree (\fB\-t\fR) from which you want to prune taxa.
-.PP
-This is RnR\-prune version 1.0 released by Andre J. Aberer in 2011\-10\-25.
-.PP
This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best\-known ML/MP\-tree).
-.PP
-SYNTAX: ./rnr\-prune [\-i <bootTrees> | \fB\-t\fR <treeFile>] \fB\-x\fR <excludeFile> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
-.IP
-OBLIGATORY:
-.PP
+.SH OPTIONS
+.SS OBLIGATORY
+.TP
\fB\-x\fR <excludeFile>
-.IP
A list of taxa (one taxon per line) to prune from either the bootstrap trees or the single best\-known tree.
-.PP
+.TP
\fB\-i\fR <bootTrees>
-.IP
A collection of bootstrap trees.
-.PP
+.TP
\fB\-t\fR <treeFile>
-.IP
A single tree with branch lengths. Use either this flag or the \fB\-i\fR flag.
-.PP
+.TP
\fB\-n\fR <runId>
-.IP
An identifier for this run.
-.IP
-OPTIONAL:
-.PP
+.SS OPTIONAL
+.TP
\fB\-w\fR <workDir>
-.IP
A working directory where output files are created.
-.PP
+.TP
\fB\-h\fR
-.IP
This help file.
.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/mans/rnr-tii.1 b/debian/mans/rnr-tii.1
index a3c0111..d5e02bf 100644
--- a/debian/mans/rnr-tii.1
+++ b/debian/mans/rnr-tii.1
@@ -1,40 +1,29 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH RNR-TII "1" "March 2017" "rnr-tii 1.0" "User Commands"
.SH NAME
rnr-tii \- computes the taxonomic instability index
-.SH DESCRIPTION
-Please specify a file containing bootstrap trees via \fB\-i\fR.
-.PP
-This is RnR\-tii version 1.0 released by Andre J. Aberer in 2011\-10\-25.
-.PP
-This program computes the taxonomic instability index.
-.PP
-SYNTAX: ./rnr\-tii \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-x <excludeFile>]
-.PP
-OBLIGATORY:
+.SH SYNOPSIS
+.B rnr\-tii
+\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-w <workingDir>] [\-h] [\-x <excludeFile>]
+.SH OPTIONS
+.SS OBLIGATORY
+.TP
\fB\-i\fR <bootTrees>
-.IP
A collection of bootstrap trees.
-.PP
+.TP
\fB\-n\fR <runId>
-.IP
An identifier for this run.
-.PP
-OPTIONAL
+.SS OPTIONAL
+.TP
\fB\-z\fR <z>
-.IP
The exponent used in the TII formula. Use small values to emphasize close relationships and vice versa. DEFAULT: 2
-.PP
+.TP
\fB\-w\fR <workDir>
-.IP
A working directory where output files are created.
-.PP
+.TP
\fB\-x\fR <excludeFile>
-.IP
Exclude the taxa in this file (one taxon per line) prior to computing the TII.
-.PP
+.TP
\fB\-h\fR
-.IP
This help file.
.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/mans/roguenarok-parallel.1 b/debian/mans/roguenarok-parallel.1
index ae72829..63b6f6e 100644
--- a/debian/mans/roguenarok-parallel.1
+++ b/debian/mans/roguenarok-parallel.1
@@ -1,82 +1,65 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH ROGUENAROK-PARALLEL "1" "March 2017" "roguenarok-parallel 1.0" "User Commands"
.SH NAME
-roguenarok-parallel \- computes the taxonomic instability index (parallel version)
-.SH DESCRIPTION
-roguenarok\-parallel: invalid option \fB\-\-\fR '\-'
-.PP
-This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011\-10\-25.
-.PP
-This program implements the RogueNaRok algorithm for rogue taxon identification.
-.PP
-SYNTAX: ./RogueNaRok \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
-.IP
-OBLIGATORY:
-.PP
+roguenarok-parallel \- implements the RogueNaRok algorithm for rogue taxon identification (parallel version)
+.SH SYNOPSIS
+.B roguenarok-parallel
+\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
+.SH OPTIONS
+.SS OBLIGATORY
+.TP
\fB\-i\fR <bootTrees>
-.IP
A collection of bootstrap trees.
-.PP
+.TP
\fB\-n\fR <runId>
-.IP
An identifier for this run.
-.IP
-OPTIONAL:
-.PP
+.TP
+\fB\-T\fR <num>
+Execute RogueNaRok in parallel with <num> threads.
+.SS OPTIONAL
+.TP
\fB\-t\fR <bestKnownTree>
-.IP
If a single best\-known tree (such as an ML or MP
tree) is provided, RogueNaRok optimizes the bootstrap support in this
best\-known tree (still drawn from the bootstrap trees). The threshold
parameter is ignored.
-.PP
+.TP
\fB\-x\fR <excludeFile>
-.IP
taxa in this file (one taxon per line) will not be
considered for pruning.
-.PP
+.TP
\fB\-c\fR <threshold>
-.IP
A threshold or mode for the consensus tree that is
-.IP
optimized. Specify a value between 50 (majority rule consensus) and
100 (strict consensus) or MR (for the extended majority rule
consensus). Note that rogue taxa identified with respect to different
thresholds can vary substantially. DEFAULT: MR consensus
-.PP
+.TP
\fB\-b\fR
-.IP
Instead of trying to maximize the support in the consensus tree,
the RogueNaRok will try to maximize the number of bipartition in the
final tree by pruning taxa. DEFAULT: off
-.PP
+.TP
\fB\-L\fR <factor>
-.IP
a weight factor to penalize for dropset size.
Factor=1 is Pattengale's criterion. The higher the value, the more
conservative the algorithm is in pruning taxa. DEFAULT: 0.0 (=RBIC)
-.PP
+.TP
\fB\-s\fR <dropsetSize>
-.IP
maximum size of dropset per iteration. If
dropsetSize == n, then RogueNaRok will test in each iteration which
tuple of n taxa increases optimality criterion the most and prunes
taxa accordingly. This improves the result, but runtimes will
increase at least linearly. DEFAULT: 1
-.PP
+.TP
\fB\-w\fR <workDir>
-.IP
A working directory where output files are created.
-.PP
-\fB\-T\fR <num>
-.IP
-Execute RogueNaRok in parallel with <num> threads. You need to compile the program for parallel execution first.
-.PP
+.TP
\fB\-h\fR
-.IP
This help file.
-.PP
-MINIMAL EXAMPLE:
-\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
+.SH EXAMPLES
+.IP
+roguenarok-parallel -T2 \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
.SH AUTHOR
+RogueNaRok was released by Andre J. Aberer in 2011\-10\-25.
+.P
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/mans/roguenarok-single.1 b/debian/mans/roguenarok-single.1
index f44e09e..fd6ff1e 100644
--- a/debian/mans/roguenarok-single.1
+++ b/debian/mans/roguenarok-single.1
@@ -1,82 +1,62 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH ROGUENAROK-SINGLE "1" "March 2017" "roguenarok-single 1.0" "User Commands"
.SH NAME
-roguenarok-single \- computes the taxonomic instability index (single core version)
-.SH DESCRIPTION
-ERROR: Please specify a file containing bootstrap trees via \fB\-i\fR.
-.PP
-This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011\-10\-25.
-.PP
-This program implements the RogueNaRok algorithm for rogue taxon identification.
-.PP
-SYNTAX: ./RogueNaRok \fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
-.IP
-OBLIGATORY:
-.PP
+roguenarok-single \- implements the RogueNaRok algorithm for rogue taxon identification (single core version)
+.SH SYNOPSIS
+.B roguenarok-single
+\fB\-i\fR <bootTrees> \fB\-n\fR <runId> [\-x <excludeFile>] [\-c <threshold>] [\-b] [\-s <dropsetSize>] [\-w <workingDir>] [\-h]
+.SH OPTIONS
+.SS OBLIGATORY
+.TP
\fB\-i\fR <bootTrees>
-.IP
A collection of bootstrap trees.
-.PP
+.TP
\fB\-n\fR <runId>
-.IP
An identifier for this run.
-.IP
-OPTIONAL:
-.PP
+.SS OPTIONAL
+.TP
\fB\-t\fR <bestKnownTree>
-.IP
If a single best\-known tree (such as an ML or MP
tree) is provided, RogueNaRok optimizes the bootstrap support in this
best\-known tree (still drawn from the bootstrap trees). The threshold
parameter is ignored.
-.PP
+.TP
\fB\-x\fR <excludeFile>
-.IP
taxa in this file (one taxon per line) will not be
considered for pruning.
-.PP
+.TP
\fB\-c\fR <threshold>
-.IP
A threshold or mode for the consensus tree that is
-.IP
optimized. Specify a value between 50 (majority rule consensus) and
100 (strict consensus) or MR (for the extended majority rule
consensus). Note that rogue taxa identified with respect to different
thresholds can vary substantially. DEFAULT: MR consensus
-.PP
+.TP
\fB\-b\fR
-.IP
Instead of trying to maximize the support in the consensus tree,
the RogueNaRok will try to maximize the number of bipartition in the
final tree by pruning taxa. DEFAULT: off
-.PP
+.TP
\fB\-L\fR <factor>
-.IP
a weight factor to penalize for dropset size.
Factor=1 is Pattengale's criterion. The higher the value, the more
conservative the algorithm is in pruning taxa. DEFAULT: 0.0 (=RBIC)
-.PP
+.TP
\fB\-s\fR <dropsetSize>
-.IP
maximum size of dropset per iteration. If
dropsetSize == n, then RogueNaRok will test in each iteration which
tuple of n taxa increases optimality criterion the most and prunes
taxa accordingly. This improves the result, but runtimes will
increase at least linearly. DEFAULT: 1
-.PP
+.TP
\fB\-w\fR <workDir>
-.IP
A working directory where output files are created.
-.PP
-\fB\-T\fR <num>
-.IP
-Execute RogueNaRok in parallel with <num> threads. You need to compile the program for parallel execution first.
-.PP
+.TP
\fB\-h\fR
-.IP
This help file.
-.PP
-MINIMAL EXAMPLE:
-\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
+.SH EXAMPLES
+.IP
+roguenarok-single \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
.SH AUTHOR
+RogueNaRok was released by Andre J. Aberer in 2011\-10\-25.
+.P
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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