[med-svn] r5469 - trunk/packages/pal2nal/trunk/debian

[Steffen Möller]

Author: moeller
Date: 2010-11-23 15:43:13 +0000 (Tue, 23 Nov 2010)
New Revision: 5469

Added:
   trunk/packages/pal2nal/trunk/debian/manpages
   trunk/packages/pal2nal/trunk/debian/pal2nal.1
Modified:
   trunk/packages/pal2nal/trunk/debian/
   trunk/packages/pal2nal/trunk/debian/README.Debian
Log:
Added man page.



Property changes on: trunk/packages/pal2nal/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Modified: trunk/packages/pal2nal/trunk/debian/README.Debian
===================================================================
--- trunk/packages/pal2nal/trunk/debian/README.Debian	2010-11-23 15:37:36 UTC (rev 5468)
+++ trunk/packages/pal2nal/trunk/debian/README.Debian	2010-11-23 15:43:13 UTC (rev 5469)
@@ -4,4 +4,8 @@
 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

Added: trunk/packages/pal2nal/trunk/debian/manpages
===================================================================
--- trunk/packages/pal2nal/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/manpages	2010-11-23 15:43:13 UTC (rev 5469)
@@ -0,0 +1 @@
+debian/pal2nal.1

Added: trunk/packages/pal2nal/trunk/debian/pal2nal.1
===================================================================
--- trunk/packages/pal2nal/trunk/debian/pal2nal.1	                        (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/pal2nal.1	2010-11-23 15:43:13 UTC (rev 5469)
@@ -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.