[med-svn] r12065 - trunk/packages/rdp-classifier/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-08-15 11:53:40 +0000 (Wed, 15 Aug 2012)
New Revision: 12065

Added:
   trunk/packages/rdp-classifier/trunk/debian/manpages
   trunk/packages/rdp-classifier/trunk/debian/rdp_classifier.1
Log:
help2html-ed + polished manpage


Added: trunk/packages/rdp-classifier/trunk/debian/manpages
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/rdp-classifier/trunk/debian/manpages	2012-08-15 11:53:40 UTC (rev 12065)
@@ -0,0 +1 @@
+debian/*.1

Added: trunk/packages/rdp-classifier/trunk/debian/rdp_classifier.1
===================================================================
--- trunk/packages/rdp-classifier/trunk/debian/rdp_classifier.1	                        (rev 0)
+++ trunk/packages/rdp-classifier/trunk/debian/rdp_classifier.1	2012-08-15 11:53:40 UTC (rev 12065)
@@ -0,0 +1,69 @@
+.TH COMMAND "1" "August 2012" "2.5" "User Commands"
+.SH NAME
+rdp_classifier \- taxonomic assignment from next generation sequencing
+.SH USAGE:
+\fBrdp_classifier\fR [\-f <arg>] [\-g <arg>] [\-o <arg>] [\-q <arg>] [\-t <arg>] [\-w <arg>]
+.SH DESCRIPTION
+The RDP Classifier is a nave Bayesian classifier that can rapidly and
+accurately provides taxonomic assignments from domain to genus, with
+confidence estimates for each assignment.
+.TP
+\fB\-f\fR,\-\-format <arg>
+all tab delimited output format: [allrank|fixrank|db]. Default is allrank.
+allrank: outputs the results for all ranks applied for each sequence: seqname, orientation,
+taxon name, rank, conf, ...
+fixrank: only outputs the results for fixed ranks in order: domain, phylum, class, order,
+family, genus
+db: outputs the seqname, trainset_no, tax_id, conf. This is good for storing in a database
+.TP
+\fB\-g\fR,\-\-gene <arg>
+16srrna|fungallsu, the default training model for 16S rRNA or Fungal LSU genes. This option
+will be overwritten by \fB\-\-train_propfile\fR option
+.TP
+\fB\-o\fR,\-\-outputFile <arg>
+output file name for classification assignment
+.TP
+\fB\-q\fR,\-\-queryFile <arg>
+query file contains sequences in one of the following formats: Fasta, Genbank and EMBL
+.TP
+\fB\-t\fR,\-\-train_propfile <arg>
+specify a property file contains the mapping of the training files if it's located outside
+of data/classifier/.
+Note: the training files and the property file should be in the same directory.
+The default property file is set to data/classifier/16srrna/rRNAClassifier.properties.
+.TP
+\fB\-w\fR,\-\-minWords <arg>
+minimum number of words for each bootstrap trial, Default is 1/8 of the words. Minimum is 5
+.PP
+usage: ClassifierCmd [\-f <arg>] [\-g <arg>] [\-o <arg>] [\-q <arg>] [\-t <arg>] [\-w <arg>]
+.TP
+\fB\-f\fR,\-\-format <arg>
+all tab delimited output format: [allrank|fixrank|db]. Default is allrank.
+allrank: outputs the results for all ranks applied for each sequence: seqname, orientation,
+taxon name, rank, conf, ...
+fixrank: only outputs the results for fixed ranks in order: domain, phylum, class, order,
+family, genus
+db: outputs the seqname, trainset_no, tax_id, conf. This is good for storing in a database
+.TP
+\fB\-g\fR,\-\-gene <arg>
+16srrna|fungallsu, the default training model for 16S rRNA or Fungal LSU genes. This option
+will be overwritten by \fB\-\-train_propfile\fR option
+.TP
+\fB\-o\fR,\-\-outputFile <arg>
+output file name for classification assignment
+.TP
+\fB\-q\fR,\-\-queryFile <arg>
+query file contains sequences in one of the following formats: Fasta, Genbank and EMBL
+.TP
+\fB\-t\fR,\-\-train_propfile <arg>
+specify a property file contains the mapping of the training files if it's located outside
+of data/classifier/.
+Note: the training files and the property file should be in the same directory.
+The default property file is set to data/classifier/16srrna/rRNAClassifier.properties.
+.TP
+\fB\-w\fR,\-\-minWords <arg>
+minimum number of words for each bootstrap trial, Default is 1/8 of the words. Minimum is 5
+.SH AUTHOR
+This manual page was generated using help2man and polished by
+Andreas Tille <tille at debian.org>, for the Debian project
+(but may be used by others).