[med-svn] [roguenarok] 01/02: Create 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 226622f798ec15311dec53ad7f4503bffe353933
Author: Andreas Tille <tille at debian.org>
Date: Tue Mar 14 11:32:27 2017 +0100
Create manpages
---
debian/createmanpages | 52 +++++++++++++++++++++++++
debian/mans/rnr-lsi.1 | 38 ++++++++++++++++++
debian/mans/rnr-mast.1 | 47 ++++++++++++++++++++++
debian/mans/rnr-prune.1 | 42 ++++++++++++++++++++
debian/mans/rnr-tii.1 | 40 +++++++++++++++++++
debian/mans/roguenarok-parallel.1 | 82 +++++++++++++++++++++++++++++++++++++++
debian/mans/roguenarok-single.1 | 82 +++++++++++++++++++++++++++++++++++++++
7 files changed, 383 insertions(+)
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..f1dff8c
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,52 @@
+#!/bin/sh
+MANDIR=debian/mans
+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 $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=roguenarok-parallel
+help2man --no-info --no-discard-stderr --help-option=" --help" \
+ --name='computes the taxonomic instability index (parallel version)' \
+ --version-string="$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)' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=rnr-lsi
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --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=" " \
+ --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=" " \
+ --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=" " \
+ --name='computes the taxonomic instability index' \
+ --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/mans/rnr-lsi.1 b/debian/mans/rnr-lsi.1
new file mode 100644
index 0000000..511ddb1
--- /dev/null
+++ b/debian/mans/rnr-lsi.1
@@ -0,0 +1,38 @@
+.\" 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
+\fB\-i\fR <bootTrees>
+.IP
+A collection of bootstrap trees.
+.PP
+\fB\-n\fR <runId>
+.IP
+An identifier for this run.
+.IP
+OPTIONAL:
+.PP
+\fB\-x\fR <excludeFile>
+.IP
+Prune the taxa in the file first (one taxon per line), before computing the lsi.
+.PP
+\fB\-w\fR <workDir>
+.IP
+A working directory where output files are created.
+.PP
+\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
new file mode 100644
index 0000000..cb88bc6
--- /dev/null
+++ b/debian/mans/rnr-mast.1
@@ -0,0 +1,47 @@
+.\" 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:
+\fB\-i\fR <bootTrees>
+.IP
+A collection of bootstrap trees.
+.PP
+\fB\-n\fR <runId>
+.IP
+An identifier for this run.
+.PP
+OPTIONAL
+\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
+\fB\-w\fR <workDir>
+.IP
+A working directory where output files are created.
+.PP
+\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
+\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
new file mode 100644
index 0000000..7562b2d
--- /dev/null
+++ b/debian/mans/rnr-prune.1
@@ -0,0 +1,42 @@
+.\" 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 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
+\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
+\fB\-i\fR <bootTrees>
+.IP
+A collection of bootstrap trees.
+.PP
+\fB\-t\fR <treeFile>
+.IP
+A single tree with branch lengths. Use either this flag or the \fB\-i\fR flag.
+.PP
+\fB\-n\fR <runId>
+.IP
+An identifier for this run.
+.IP
+OPTIONAL:
+.PP
+\fB\-w\fR <workDir>
+.IP
+A working directory where output files are created.
+.PP
+\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
new file mode 100644
index 0000000..a3c0111
--- /dev/null
+++ b/debian/mans/rnr-tii.1
@@ -0,0 +1,40 @@
+.\" 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:
+\fB\-i\fR <bootTrees>
+.IP
+A collection of bootstrap trees.
+.PP
+\fB\-n\fR <runId>
+.IP
+An identifier for this run.
+.PP
+OPTIONAL
+\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
+\fB\-w\fR <workDir>
+.IP
+A working directory where output files are created.
+.PP
+\fB\-x\fR <excludeFile>
+.IP
+Exclude the taxa in this file (one taxon per line) prior to computing the TII.
+.PP
+\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
new file mode 100644
index 0000000..ae72829
--- /dev/null
+++ b/debian/mans/roguenarok-parallel.1
@@ -0,0 +1,82 @@
+.\" 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
+\fB\-i\fR <bootTrees>
+.IP
+A collection of bootstrap trees.
+.PP
+\fB\-n\fR <runId>
+.IP
+An identifier for this run.
+.IP
+OPTIONAL:
+.PP
+\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
+\fB\-x\fR <excludeFile>
+.IP
+taxa in this file (one taxon per line) will not be
+considered for pruning.
+.PP
+\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
+\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
+\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
+\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
+\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
+\fB\-h\fR
+.IP
+This help file.
+.PP
+MINIMAL EXAMPLE:
+\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
+.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-single.1 b/debian/mans/roguenarok-single.1
new file mode 100644
index 0000000..f44e09e
--- /dev/null
+++ b/debian/mans/roguenarok-single.1
@@ -0,0 +1,82 @@
+.\" 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
+\fB\-i\fR <bootTrees>
+.IP
+A collection of bootstrap trees.
+.PP
+\fB\-n\fR <runId>
+.IP
+An identifier for this run.
+.IP
+OPTIONAL:
+.PP
+\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
+\fB\-x\fR <excludeFile>
+.IP
+taxa in this file (one taxon per line) will not be
+considered for pruning.
+.PP
+\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
+\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
+\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
+\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
+\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
+\fB\-h\fR
+.IP
+This help file.
+.PP
+MINIMAL EXAMPLE:
+\&./RogueNaRok \fB\-i\fR <bootstrapTreeFile> \fB\-n\fR run1
+.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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