[med-svn] r12954 - trunk/packages/boxshade/trunk/debian
Charles Plessy
plessy at alioth.debian.org
Sat Feb 9 04:55:45 UTC 2013
Author: plessy
Date: 2013-02-09 04:55:44 +0000 (Sat, 09 Feb 2013)
New Revision: 12954
Modified:
trunk/packages/boxshade/trunk/debian/boxshade.1
trunk/packages/boxshade/trunk/debian/boxshade.1.xml
Log:
Added command line parameters to manual page.
Modified: trunk/packages/boxshade/trunk/debian/boxshade.1
===================================================================
--- trunk/packages/boxshade/trunk/debian/boxshade.1 2013-02-09 03:57:03 UTC (rev 12953)
+++ trunk/packages/boxshade/trunk/debian/boxshade.1 2013-02-09 04:55:44 UTC (rev 12954)
@@ -2,12 +2,12 @@
.\" Title: BOXSHADE
.\" Author: Kay Hofmann <kay.hofmann at memorec.com>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\" Date: February 23, 2007
+.\" Date: February 09, 2013
.\" Manual: Boxshade Manual
-.\" Source: boxshade 3.3
+.\" Source: boxshade 3.3.1
.\" Language: English
.\"
-.TH "BOXSHADE" "1" "February 23, 2007" "boxshade 3.3" "Boxshade Manual"
+.TH "BOXSHADE" "1" "February 09, 2013" "boxshade 3.3.1" "Boxshade Manual"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -37,6 +37,136 @@
\fBBOXSHADE\fR
is a program for pretty\-printing multiple alignment output\&. The program itself doesn\*(Aqt do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE\&.
.PP
+\fB\-help\fR
+.RS 4
+Show the help\&.
+.RE
+.PP
+\fB \-check \fR
+.RS 4
+Show the help and extend command line\&.
+.RE
+.PP
+\fB \-def \fR
+.RS 4
+Use defaults, no unnecessary questions\&.
+.RE
+.PP
+\fB \-numdef \fR
+.RS 4
+Use default numbering\&.
+.RE
+.PP
+\fB \-dna \fR
+.RS 4
+Assume DNA sequences, use
+box_dna\&.par\&.
+.RE
+.PP
+\fB \-split \fR
+.RS 4
+Create separate files for multiple pages\&.
+.RE
+.PP
+\fB \-toseq=\fR\fB\fIxxx\fR\fR\fB \fR
+.RS 4
+Shading according to sequence No\&.
+\fIxxx\fR\&.
+.RE
+.PP
+\fB \-in=\fR\fB\fIxxxxx\fR\fR\fB \fR
+.RS 4
+
+\fIxxxxx\fR
+is input file name\&.
+.RE
+.PP
+\fB \-out=\fR\fB\fIxxxxx\fR\fR\fB \fR
+.RS 4
+
+\fIxxxxx\fR
+is output file name\&.
+.RE
+.PP
+\fB \-par=\fR\fB\fIxxxxx\fR\fR\fB \fR
+.RS 4
+
+\fIxxxxx\fR
+is parameter file name\&.
+.RE
+.PP
+\fB \-sim=\fR\fB\fIxxxxx\fR\fR\fB \fR
+.RS 4
+
+\fIxxxxx\fR
+is file name for similar residues def\&.
+.RE
+.PP
+\fB \-grp=\fR\fB\fIxxxxx\fR\fR\fB \fR
+.RS 4
+
+\fIxxxxx\fR
+is file name for grouping residues def\&.
+.RE
+.PP
+\fB \-thr=\fR\fB\fIx\fR\fR\fB \fR
+.RS 4
+
+\fIx\fR
+is the fraction of sequences that must agree for a consensus\&.
+.RE
+.PP
+\fB \-dev=\fR\fB\fIx\fR\fR\fB \fR
+.RS 4
+
+\fIx\fR
+is output device class (see below)\&.
+.RE
+.PP
+\fB \-type=\fR\fB\fIx\fR\fR\fB \fR
+.RS 4
+
+\fIx\fR
+is input file format (see below)\&.
+.RE
+.PP
+\fB \-ruler \fR
+.RS 4
+Print ruler line\&.
+.RE
+.PP
+\fB \-cons \fR
+.RS 4
+Create consensus line\&.
+.RE
+.PP
+\fB \-symbcons=\fR\fB\fIxyz\fR\fR\fB \fR
+.RS 4
+
+\fIxyz\fR
+are consensus symbols\&.
+.RE
+.PP
+\fB \-symbcons="\fR\fB\fIxyz\fR\fR\fB" \fR
+.RS 4
+If the one above does not work, try this one\&.
+.RE
+.PP
+\fB \-unix \fR
+.RS 4
+Output files lines are terminated with LF only\&.
+.RE
+.PP
+\fB \-mac \fR
+.RS 4
+Output files lines are terminated with CR only\&.
+.RE
+.PP
+\fB \-dos \fR
+.RS 4
+Output files lines are terminated with CRLF\&.
+.RE
+.PP
This manual page was written for the
Debian(TM)
distribution because the original program does not have a manual page\&. The presented information comes from the documentation of the Web Service of the 3\&.21 version that is not available as a Debian package\&.
@@ -129,12 +259,12 @@
C port of Boxshade\&. (don\*(Aqt send Kay or Michael any questions concerning the \*(AqC\*(Aq version of boxshade)
.RE
.PP
-\fBSteffen Möller\fR <\&steffen_moeller at gmx\&.de\&>
+\fBSteffen Möller\fR <\&moeller at debian\&.org\&>
.RS 4
Wrote the manpage\&.
.RE
.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\&.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.RS 4
Updated the manpage
.RE
Modified: trunk/packages/boxshade/trunk/debian/boxshade.1.xml
===================================================================
--- trunk/packages/boxshade/trunk/debian/boxshade.1.xml 2013-02-09 03:57:03 UTC (rev 12953)
+++ trunk/packages/boxshade/trunk/debian/boxshade.1.xml 2013-02-09 04:55:44 UTC (rev 12954)
@@ -15,13 +15,13 @@
<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
<!ENTITY dhsurname "<surname>Möller</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "February 23, 2007">
+ <!ENTITY dhdate "February 09, 2013">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>steffen_moeller at gmx.de</email>">
+ <!ENTITY dhemail "<email>moeller at debian.org</email>">
<!ENTITY dhusername "Steffen Moeller">
<!ENTITY dhucpackage "<refentrytitle>BOXSHADE</refentrytitle>">
<!ENTITY dhpackage "boxshade">
- <!ENTITY dhrelease "3.3">
+ <!ENTITY dhrelease "3.3.1">
<!ENTITY dhtitle "Boxshade Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
@@ -100,7 +100,7 @@
</contrib>
<address>
<email>
- charles-debian-nospam at plessy.org
+ plessy at debian.org
</email>
</address>
</author>
@@ -148,6 +148,268 @@
<title>DESCRIPTION</title>
<para><command>BOXSHADE</command> is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE.</para>
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-help</option>
+ </term>
+ <listitem>
+ <para>
+ Show the help.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -check
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Show the help and extend command line.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -def
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Use defaults, no unnecessary questions.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -numdef
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Use default numbering.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -dna
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Assume DNA sequences, use <filename>box_dna.par</filename>.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -split
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Create separate files for multiple pages.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -toseq=<replaceable class="parameter">xxx</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Shading according to sequence No. <replaceable class="parameter">xxx</replaceable>.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -in=<replaceable class="parameter">xxxxx</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">xxxxx</replaceable> is input file name.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -out=<replaceable class="parameter">xxxxx</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">xxxxx</replaceable> is output file name.
+ </para>
+ </listitem>
+ </varlistentry><varlistentry>
+ <term>
+ <option>
+ -par=<replaceable class="parameter">xxxxx</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">xxxxx</replaceable> is parameter file name.
+ </para>
+ </listitem>
+ </varlistentry><varlistentry>
+ <term>
+ <option>
+ -sim=<replaceable class="parameter">xxxxx</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">xxxxx</replaceable> is file name for similar residues def.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -grp=<replaceable class="parameter">xxxxx</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">xxxxx</replaceable> is file name for grouping residues def.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -thr=<replaceable class="parameter">x</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">x</replaceable> is the fraction of sequences that must agree for a consensus.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -dev=<replaceable class="parameter">x</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">x</replaceable> is output device class (see below).
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -type=<replaceable class="parameter">x</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">x</replaceable> is input file format (see below).
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -ruler
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Print ruler line.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -cons
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Create consensus line.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -symbcons=<replaceable class="parameter">xyz</replaceable>
+ </option>
+ </term>
+ <listitem>
+ <para>
+ <replaceable class="parameter">xyz</replaceable> are consensus symbols.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -symbcons="<replaceable class="parameter">xyz</replaceable>"
+ </option>
+ </term>
+ <listitem>
+ <para>
+ If the one above does not work, try this one.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -unix
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Output files lines are terminated with LF only.
+ </para>
+ </listitem>
+ </varlistentry><varlistentry>
+ <term>
+ <option>
+ -mac
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Output files lines are terminated with CR only.
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>
+ -dos
+ </option>
+ </term>
+ <listitem>
+ <para>
+ Output files lines are terminated with CRLF.
+ </para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+
<para>This manual page was written for the &debian; distribution
because the original program does not have a manual page. The presented information comes from the documentation of the Web Service of the 3.21 version that is not available as a Debian package.
</para>
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