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 <[email protected]> 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. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
