[med-svn] r13832 - trunk/packages/microbiomeutil/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-06-04 15:00:12 +0000 (Tue, 04 Jun 2013)
New Revision: 13832

Added:
   trunk/packages/microbiomeutil/trunk/debian/wigeon.1
   trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages
Modified:
   trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links
Log:
wigeon.1


Modified: trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links	2013-06-04 14:34:57 UTC (rev 13831)
+++ trunk/packages/microbiomeutil/trunk/debian/microbiomeutil.links	2013-06-04 15:00:12 UTC (rev 13832)
@@ -3,3 +3,4 @@
 usr/bin/wigeon		usr/bin/WigeoN
 usr/share/man/man1/chimeraslayer.1.gz	usr/share/man/man1/ChimeraSlayer.1.gz
 usr/share/man/man1/nast-ier.1.gz	usr/share/man/man1/NAST-iEr.1.gz
+usr/share/man/man1/wigeon.1.gz		usr/share/man/man1/WigeoN.1.gz

Added: trunk/packages/microbiomeutil/trunk/debian/wigeon.1
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/wigeon.1	                        (rev 0)
+++ trunk/packages/microbiomeutil/trunk/debian/wigeon.1	2013-06-04 15:00:12 UTC (rev 13832)
@@ -0,0 +1,44 @@
+.TH WIGEON "1" "June 2013" "wigeon " "User Commands"
+.SH NAME
+wigeon \- reimplementation of the Pintail 16S DNA anomaly detection utility
+.SH DESCRIPTION
+WigeoN examines the sequence conservation between a query and a trusted
+reference sequence, both in NAST alignment format. Based on the sequence
+identity between the query and the reference sequence, there is an
+expected amount of variation among the alignment. If the observed
+variation is greater than the 95% quantile of the distribution of
+variation observed between non-anomalous sequences, then it is flagged
+as an anomaly.
+.PP
+WigeoN is a flexible command-line based reimplementation of the Pintail
+algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36.
+.PP
+WigeoN is useful for flagging chimeras and anomalies only in near
+full-length 16S rRNA sequences. WigeoN lacks sensitivity with sequences
+less than 1000 bp.
+.PP
+To run WigeoN, you need NAST-formatted sequences generated by the
+nast-ier utility.
+.PP
+WigeoN is  part of the microbiomeutil suite.
+.SH OPTIONS
+.SS Required:
+.IP \fB\-\-query_NAST\fR
+multi\-fasta file containing query sequences in alignment format
+.SS Optional:
+.IP \fB\-\-db_NAST\fR
+db in NAST format
+.IP \fB\-\-db_FASTA\fR
+db in fasta format (megablast formatted)
+.IP \fB\-\-num_top_hits\fR
+default 1: uses only the single best match.
+.IP \fB\-\-plot\fR
+.IP \fB\-\-DEBUG\fR
+.IP \fB\-\-exec_dir\fR
+cd to exec_dir before running
+.PP
+.SH "SEE ALSO"
+http://microbiomeutil.sourceforge.net/#A_WigeoN
+.SH AUTHOR
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.

Added: trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages	                        (rev 0)
+++ trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages	2013-06-04 15:00:12 UTC (rev 13832)
@@ -0,0 +1 @@
+debian/wigeon.1