[med-svn] [fastml] 01/01: (quite ugly) manpages (but I tried my best ...)
Andreas Tille
tille at debian.org
Wed Nov 18 19:45:15 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fastml.
commit ef6fe0c9ed6f4ac7f7190ffa3725b2d0254e4031
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 18 20:44:44 2015 +0100
(quite ugly) manpages (but I tried my best ...)
---
debian/createmanpages | 34 +++++++++++++++++
debian/fastml.1 | 100 ++++++++++++++++++++++++++++++++++++++++++++++++++
debian/gainLoss.1 | 41 +++++++++++++++++++++
debian/indelCoder.1 | 13 +++++++
debian/manpages | 1 +
5 files changed, 189 insertions(+)
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..48ee4f7
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,34 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+for bin in fastml gainLoss indelCoder ; do
+ echo "cat debian/${bin}.out" > debian/${bin}.sh
+ chmod 755 debian/${bin}.sh
+ ${bin} 2>&1 | tee | \
+ sed -e 's/^ *+--\++ *//' -e 's/|\(.*[^ ]\) *|/\1/' | \
+ grep -v -- '-------- HELP: ----------' \
+ > debian/${bin}.out
+done
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='maximum likelihood ancestral amino-acid sequence reconstruction' \
+ --version-string="$VERSION" debian/fastml.sh > $MANDIR/fastml.1
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='Analysis of Phyletic Patterns in a Likelihood Framework' \
+ --version-string="$VERSION" debian/gainLoss.sh > $MANDIR/gainLoss.1
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='FastML indelCoder' \
+ --version-string="$VERSION" debian/indelCoder.sh > $MANDIR/indelCoder.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+rm debian/*.out debian/*.sh
diff --git a/debian/fastml.1 b/debian/fastml.1
new file mode 100644
index 0000000..7fb2f64
--- /dev/null
+++ b/debian/fastml.1
@@ -0,0 +1,100 @@
+.TH FASTML.SH "1" "November 2015" "fastml.sh 3.1" "User Commands"
+.SH NAME
+fastml \- maximum likelihood ancestral amino-acid sequence reconstruction
+.SH SYNOPSIS
+.B fastml
+\fI[options]\fR
+.SH DESCRIPTION
+FastML is a bioinformatics tool for the reconstruction of ancestral
+sequences based on the phylogenetic relations between homologous
+sequences. FastML runs several algorithms that reconstruct the ancestral
+sequences with emphasis on an accurate reconstruction of both indels and
+characters. For character reconstruction the previously described FastML
+algorithms are used to efficiently infer the most likely ancestral
+sequences for each internal node of the tree. Both joint and the
+marginal reconstructions are provided. For indels reconstruction the
+sequences are first coded according to the indel events detected within
+the multiple sequence alignment (MSA) and then a state-of-the-art
+likelihood model is used to reconstruct ancestral indels states. The
+results are the most probable sequences, together with posterior
+probabilities for each character and indel at each sequence position for
+each internal node of the tree. FastML is generic and is applicable for
+any type of molecular sequences (nucleotide, protein, or codon
+sequences).
+.SH OPTIONS
+.TP
+\fB\-h\fR help
+.TP
+\fB\-s\fR sequence input file (for example use \fB\-s\fR emySequences/eseq.txt)
+.TP
+\fB\-t\fR tree input file (if tree is not given, a neighbor joining tree is computed).
+.TP
+\fB\-g\fR Assume among site rate variation model (Gamma) [By default the program
+will assume an homogenous model. very fast, but less accurate!]
+.TP
+\fB\-m\fR model name
+.TP
+\fB\-mj\fR [JTT]
+.TP
+\fB\-ml\fR LG
+.TP
+\fB\-mr\fR mtREV (for mitochondrial genomes)
+.TP
+\fB\-md\fR DAY
+.TP
+\fB\-mw\fR WAG
+.TP
+\fB\-mc\fR cpREV (for chloroplasts genomes)
+.TP
+\fB\-ma\fR Jukes and Cantor (JC) for amino acids
+.TP
+\fB\-mn\fR Jukes and Cantor (JC) for nucleotides
+.TP
+\fB\-mh\fR HKY Model for nucleotides
+.TP
+\fB\-mg\fR nucgtr Model for nucleotides
+.TP
+\fB\-mt\fR tamura92 Model for nucleotides
+.TP
+\fB\-my\fR yang M5 codons model
+.TP
+\fB\-me\fR empirical codon matrix
+.PP
+Controling the output options:
+.TP
+\fB\-x\fR tree file output in Newick format [tree.newick.txt]
+.TP
+\fB\-y\fR tree file output in ANCESTOR format [tree.ancestor.txt]
+.TP
+\fB\-j\fR joint sequences output file [seq.joint.txt]
+.TP
+\fB\-k\fR marginal sequences output file [seq.marginal.txt]
+.TP
+\fB\-d\fR joint probabilities output file [prob.joint.txt]
+.TP
+\fB\-e\fR marginal probabilities output file [prob.marginal.txt]
+.TP
+\fB\-q\fR ancestral sequences output format. (\fB\-qc\fR = [CLUSTAL], \fB\-qf\fR = FASTA,
+\fB\-qm\fR = MOLPHY, \fB\-qs\fR = MASE, \fB\-qp\fR = PHLIYP, \fB\-qn\fR = Nexus)
+.PP
+Advanced options:
+.TP
+\fB\-a\fR Treshold for computing again marginal probabilities [0.9]
+.TP
+\fB\-b\fR Do not optimize branch lengths on starting tree
+[by default branches and alpha are ML optimized from the data]
+.TP
+\fB\-c\fR
+number of discrete Gamma categories for the gamma distribution [8]
+.TP
+\fB\-f\fR
+don't compute Joint reconstruction (good if the branch and bound
+algorithm takes too much time, and the goal is to compute the
+marginal reconstruction with Gamma).
+.TP
+\fB\-z\fR
+The bound used. \fB\-zs\fR \- bound based on sum. \fB\-zm\fR based on max. \fB\-zb\fR [both]
+.TP
+\fB\-p\fR
+user alpha parameter of the gamma distribution [if alpha is not given,
+alpha and branches will be evaluated from the data (override \fB\-b\fR)
diff --git a/debian/gainLoss.1 b/debian/gainLoss.1
new file mode 100644
index 0000000..a8e24fd
--- /dev/null
+++ b/debian/gainLoss.1
@@ -0,0 +1,41 @@
+.TH GAINLOSS.SH "1" "November 2015" "gainLoss.sh 3.1" "User Commands"
+.SH NAME
+gainLoss \- Analysis of Phyletic Patterns in a Likelihood Framework
+.SH DESCRIPTION
+The gainLoss project:
+Analysis of Phyletic Patterns in a Likelihood Framework
+Version: gainLoss.VR01.266 \- last updated 14.10.2013
+Ofir Cohen \- ofircohe at tau.ac.il
+.SH USAGE
+use a parameter file with these options:
+.PP
+_seqFile
+.PP
+_treeFile
+.IP
+_rootAt
+_logFile
+_logValue
+_referenceSeq
+_outDir
+_outFile
+_treeOutFile
+_numberOfGainCategories
+_numberOfLossCategories
+_numberOfRateCategories
+_maxNumOfIterationsModel
+_epsilonOptimizationModel
+_maxNumOfIterationsBBL
+_epsilonOptimizationBBL
+_epsilonOptimization
+.IP
+_gainLossDist
+_calculateRate4site
+_calculeGainLoss4site
+_printTree
+_printPij_t
+_printLofPos
+_performOptimizations
+_isHGT_normal_Pij
+_isReversible
+\&...(a very partial list)
diff --git a/debian/indelCoder.1 b/debian/indelCoder.1
new file mode 100644
index 0000000..218edb3
--- /dev/null
+++ b/debian/indelCoder.1
@@ -0,0 +1,13 @@
+.TH INDELCODER.SH "1" "November 2015" "indelCoder.sh 3.1" "User Commands"
+.SH NAME
+indelCoder \- FastML indelCoder
+.SH DESCRIPTION
+The indelCoder project.
+.SH USAHE
+use a parameter file with these options:
+.PP
+_seqFile
+.IP
+_logFile
+_logValue
+\&...(a partial list)
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
--
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