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 <[email protected]> .\" 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@gmx\&.de\&> +\fBSteffen Möller\fR <\&moeller@debian\&.org\&> .RS 4 Wrote the manpage\&. .RE .PP -\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy\&.org\&> +\fBCharles Plessy\fR <\&plessy@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>[email protected]</email>"> + <!ENTITY dhemail "<email>[email protected]</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> - [email protected] + [email protected] </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> _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
