[med-svn] r13865 - trunk/packages/mira/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-06-07 07:37:38 +0000 (Fri, 07 Jun 2013)
New Revision: 13865

Modified:
   trunk/packages/mira/trunk/debian/changelog
   trunk/packages/mira/trunk/debian/fastatool.1
Log:
Reviewed fastatool.1


Modified: trunk/packages/mira/trunk/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog	2013-06-07 07:30:41 UTC (rev 13864)
+++ trunk/packages/mira/trunk/debian/changelog	2013-06-07 07:37:38 UTC (rev 13865)
@@ -22,7 +22,7 @@
   [ Andreas Tille ]
   * delete debian/README.source which is outdated / wrong
   * debian/{mira.1,miradiff.1,miramer.1, scftool.1, convert_project.1,
-    fasta2frag.1, fastaselect.1}:
+    fasta2frag.1, fastaselect.1, fastatool.1}:
     Wrote manpage for some programs
   * Removed debian/obsolete.mira-assembler.install
 

Modified: trunk/packages/mira/trunk/debian/fastatool.1
===================================================================
--- trunk/packages/mira/trunk/debian/fastatool.1	2013-06-07 07:30:41 UTC (rev 13864)
+++ trunk/packages/mira/trunk/debian/fastatool.1	2013-06-07 07:37:38 UTC (rev 13865)
@@ -1,19 +1,49 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.42.1.
-.TH FASTATOOL "1" "June 2013" "fastatool" "User Commands"
+.TH FASTATOOL "1" "June 2013" "3.9.17" "User Commands"
 .SH NAME
 .B fastatool \- Provides a set of tools useful when working with FASTA files.
-.SH AUTHOR
-Written by Bastien Chevreux (bach at chevreux.org)
+.SH DESCRIPTION
+This program is part of the MIRA assembler package.
+Fastatool provides a set of tools useful when working with FASTA trace files.
 .PP
-.SH "Usage:"
-.IP
-fastatool <toolname> <tool parameters>
-.SH "Available tools:"
+Please check out the documentation below for more detailed information.
+.SH SYNOPSIS"
+fastatool \fI<toolname>\fR \fI<tool parameters>\fR
+.SH OPTIONS
 .TP
 clip
-Clip left and right parts of a FASTA sequence.
+Clips bases on the left and right of a FASTA sequence, writes result to STDOUT.
+.IP
+Usage:
 .TP
+        clipFASTA -l leftclip -r rightclip fastainfile
+.TP
 sanitize
-Deletes invalid sequences from FASTA files.
+Deletes sequences with non-IUPAC bases or empty sequences from a FASTA file,
+writes the 'surviving' sequences to a new file.
+If a quality file is given, a cleaned version of that is also written.
+The sequences in the quality files (if given) MUST be in the same order than
+in the fasta file.
+.IP
+Usage:
+.TP
+        sanitizeFASTA fastainfile fastaoutfile [fastaqualin fastaqualoutfile]
+.SH "SEE ALSO"
+A more extensive documentation is provided in the mira-doc package and can be found at
+/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
 .PP
-To get help on a specific tool, type 'fastatool <toolname>'. E.g.: fastatool cut
+You can also subscribe one of the MIRA mailing lists at
+.IP
+http://www.chevreux.org/mira_mailinglists.html
+.PP
+After subscribing, mail general questions to the MIRA talk mailing list:
+.IP
+mira_talk at freelists.org
+.SH BUGS
+To report bugs or ask for features, please use the new ticketing system at:
+.IP
+http://sourceforge.net/apps/trac/mira\-assembler/
+.SH AUTHOR
+The author of the mira code is Bastien Chevreux <bach at chevreux.org>
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.