[med-svn] r13833 - trunk/packages/microbiomeutil/trunk/debian

[Andreas Tille]

Author: tille
Date: 2013-06-04 15:18:30 +0000 (Tue, 04 Jun 2013)
New Revision: 13833

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


Added: trunk/packages/microbiomeutil/trunk/debian/cm_to_wigeon.1
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/cm_to_wigeon.1	                        (rev 0)
+++ trunk/packages/microbiomeutil/trunk/debian/cm_to_wigeon.1	2013-06-04 15:18:30 UTC (rev 13833)
@@ -0,0 +1,46 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.2.
+.TH CM_TO_WIGEON "1" "June 2013" "cm_to_wigeon " "User Commands"
+.SH NAME
+cm_to_wigeon \- helper for wigeon (Pintail 16S DNA anomaly detection)
+.SH DESCRIPTION
+\fBUnfortunately this tools that comes in connection with wigeon(1)
+is not documented but it regards the options below.  If you know
+better about its purpose please drop us a note using reportbug on
+your Debian system.\fR
+.SH OPTIONS
+.SS Required:
+.IP \fB\-\-query_NAST\fR
+multi\-fasta file containing query sequences in alignment format
+.IP \fB\-\-db_NAST\fR
+db in NAST format
+.IP \fB\-\-db_FASTA\fR
+db in fasta format (megablast formatted)
+.SS Common options
+.IP \fB\-n\fR
+number of top matching database sequences to compare to (default 15)
+.IP \fB\-R\fR
+min divergence ratio default: 1.007
+.IP \fB\-P\fR
+min percent identity among matching sequences (default 90)
+.SS Parameters to tune ChimeraMaligner:
+Scoring parameters:
+.IP \fB\-M\fR
+match score   (default: +5)
+.IP \fB\-N\fR
+mismatch penalty  (default: \fB\-4\fR)
+.IP \fB\-Q\fR
+min query coverage by matching database sequence (default: 70)
+.IP \fB\-T\fR
+maximum traverses of the multiple alignment  (default: 1)
+.SS Flags:
+.IP \fB\-\-printAlignments\fR
+(default off)
+.IP \fB\-v\fR
+verbose
+.IP \fB\-\-exec_dir\fR
+cd here before running
+.SH "SEE ALSO"
+http://microbiomeutil.sourceforge.net/
+.SH AUTHOR
+This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
+distribution.

Modified: trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages
===================================================================
--- trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages	2013-06-04 15:00:12 UTC (rev 13832)
+++ trunk/packages/microbiomeutil/trunk/debian/wigeon.manpages	2013-06-04 15:18:30 UTC (rev 13833)
@@ -1 +1,2 @@
 debian/wigeon.1
+debian/cm_to_wigeon.1