[med-svn] [pal2nal] 02/14: Added man page.

[Andreas Tille]

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

tille pushed a commit to branch master
in repository pal2nal.

commit 0cbb9223cd223cac3e5d0953a01673ddc94ca910
Author: Steffen Moeller <moeller at debian.org>
Date:   Tue Nov 23 15:43:13 2010 +0000

    Added man page.
---
 debian/README.Debian |   4 ++
 debian/manpages      |   1 +
 debian/pal2nal.1     | 107 +++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 112 insertions(+)

diff --git a/debian/README.Debian b/debian/README.Debian
index d5fef58..0146bc0 100644
--- a/debian/README.Debian
+++ b/debian/README.Debian
@@ -4,4 +4,8 @@ pal2nal for Debian
 This package comes without a license and as such remains unredistributable
 untils this has been clarified with upstream.
 
+It remains unclear if the "binary" should be renamed to pal2nal, ie.
+lose its .pl suffix. The answer is most likely "yes", but would require
+some synchronisation e.g. with the bioperl developers.
+
  -- Steffen Moeller <steffen_moeller at gmx.de>  Tue, 23 Nov 2010 16:18:36 +0100
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..7072627
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/pal2nal.1
diff --git a/debian/pal2nal.1 b/debian/pal2nal.1
new file mode 100644
index 0000000..80ebb3b
--- /dev/null
+++ b/debian/pal2nal.1
@@ -0,0 +1,107 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
+.TH PAL2NAL.PL "1" "November 2010" "pal2nal.pl " "User Commands"
+.SH NAME
+pal2nal.pl \- manual page for pal2nal.pl 
+.SH SYNOPSIS
+.B pal2nal.pl
+\fIpep.aln  nuc.fasta  \fR[\fInuc.fasta\fR...]  [\fIoptions\fR]
+.SH DESCRIPTION
+pal2nal.pl  (v13)
+.TP
+pep.aln:
+protein alignment either in CLUSTAL or FASTA format
+.TP
+nuc.fasta:
+DNA sequences (single multi\-fasta or separated files)
+.TP
+Options:
+\fB\-h\fR            Show help
+.IP
+\fB\-output\fR (clustal|paml|fasta|codon)
+.IP
+Output format; default = clustal
+.TP
+\fB\-blockonly\fR
+Show only user specified blocks
+\&'#' under CLUSTAL alignment (see example)
+.TP
+\fB\-nogap\fR
+remove columns with gaps and inframe stop codons
+.TP
+\fB\-nomismatch\fR
+remove mismatched codons (mismatch between
+pep and cDNA) from the output
+.IP
+\fB\-codontable\fR (universal|vmitochondria)
+.IP
+Codon table
+.IP
+\- universal (default)
+\- vmitochondria \-> vertebrate mitochondrial
+.TP
+\fB\-html\fR
+HTML output (only for the web server)
+.TP
+\fB\-nostderr\fR
+No STDERR messages (only for the web server)
+.IP
+\- sequence order in pep.aln and nuc.fasta should be the same.
+.IP
+\- IDs in pep.aln are used in the output.
+.PP
+pal2nal.pl  (v13)
+.PP
+Usage:  pal2nal.pl  pep.aln  nuc.fasta  [nuc.fasta...]  [options]
+.TP
+pep.aln:
+protein alignment either in CLUSTAL or FASTA format
+.TP
+nuc.fasta:
+DNA sequences (single multi\-fasta or separated files)
+.TP
+Options:
+\fB\-h\fR            Show help
+.IP
+\fB\-output\fR (clustal|paml|fasta|codon)
+.IP
+Output format; default = clustal
+.TP
+\fB\-blockonly\fR
+Show only user specified blocks
+\&'#' under CLUSTAL alignment (see example)
+.TP
+\fB\-nogap\fR
+remove columns with gaps and inframe stop codons
+.TP
+\fB\-nomismatch\fR
+remove mismatched codons (mismatch between
+pep and cDNA) from the output
+.IP
+\fB\-codontable\fR (universal|vmitochondria)
+.IP
+Codon table
+.IP
+\- universal (default)
+\- vmitochondria \-> vertebrate mitochondrial
+.TP
+\fB\-html\fR
+HTML output (only for the web server)
+.TP
+\fB\-nostderr\fR
+No STDERR messages (only for the web server)
+.IP
+\- sequence order in pep.aln and nuc.fasta should be the same.
+.IP
+\- IDs in pep.aln are used in the output.
+.SH "SEE ALSO"
+The full documentation for
+.B pal2nal.pl
+is maintained as a Texinfo manual.  If the
+.B info
+and
+.B pal2nal.pl
+programs are properly installed at your site, the command
+.IP
+.B info pal2nal.pl
+.PP
+should give you access to the complete manual.

-- 
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