[med-svn] [rambo-k] 07/09: Manpage

[Andreas Tille]

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commit 8da06e47d14a4d6dafa1d8275b2dc0eec35bcd14
Author: Andreas Tille <tille at debian.org>
Date:   Mon Nov 21 15:54:23 2016 +0100

    Manpage
---
 debian/manpages  |  1 +
 debian/rambo-k.1 | 81 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 82 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/rambo-k.1 b/debian/rambo-k.1
new file mode 100644
index 0000000..a1a9f74
--- /dev/null
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+.TH RAMBO-K "1" "November 2016" "rambo-k 1.21" "User Commands"
+.SH NAME
+rambo-k \- Read Assignment Method Based On K-mers
+.SH SYNOPSIS
+.B rambo\-k
+[\-h] \fB\-r\fR REFFILE1 \fB\-R\fR REFFILE2 [\-n NAME1] [\-N NAME2] \fB\-1\fR
+UNASSIGNED1 [\-2 UNASSIGNED2] [\-k KMERSIZES] [\-o OUTPATH]
+[\-a AMOUNT] [\-t THREADS] [\-x CHUNKSIZE] [\-g GAPSIZE]
+[\-c CUTOFF_LOWER] [\-C CUTOFF_HIGHER] [\-d] [\-f FILETYPE]
+.SH DESCRIPTION
+RAMBO-K is a reference-based tool for rapid and sensitive extraction of
+one organisms reads from a mixed dataset. It is based on a Markov chain
+implementation, which uses genomic characteristics of each reference to
+assign reads to the associated set.
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-r\fR REFFILE1, \fB\-\-reffile1\fR REFFILE1
+Reference file of species 1 in fasta\-format. Should
+pair with name1
+.TP
+\fB\-R\fR REFFILE2, \fB\-\-reffile2\fR REFFILE2
+Reference file of species 2 in fasta\-format. Should
+pair with name2
+.TP
+\fB\-n\fR NAME1, \fB\-\-name1\fR NAME1
+Name of species 1
+.TP
+\fB\-N\fR NAME2, \fB\-\-name2\fR NAME2
+Name of species 2
+.TP
+\fB\-1\fR UNASSIGNED1, \fB\-\-unassigned1\fR UNASSIGNED1
+Fasta\- or fastq\-file containing mixed reads.
+.TP
+\fB\-2\fR UNASSIGNED2, \fB\-\-unassigned2\fR UNASSIGNED2
+Fasta\- or fastq\-file containing mixed reads, only
+required in paired end mode.
+.TP
+\fB\-k\fR KMERSIZES, \fB\-\-kmersizes\fR KMERSIZES
+Order of Markov\-Chain/kmer length. Enter as range
+(e.g. 4:8) or list (e.g. 4,6,8) or integer (e.g. 8).
+Default = 8
+.TP
+\fB\-o\fR OUTPATH, \fB\-\-outpath\fR OUTPATH
+Folder to write results to. Default = $name1_$name2/
+in your working directory
+.TP
+\fB\-a\fR AMOUNT, \fB\-\-amount\fR AMOUNT
+Number of reads to be simulated, default = 50000
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+Number of Threads to use
+.TP
+\fB\-x\fR CHUNKSIZE, \fB\-\-chunksize\fR CHUNKSIZE
+Size of chunks created at a time for simulation,
+default = 100000. Only change if you know what you are
+doing!
+.TP
+\fB\-g\fR GAPSIZE, \fB\-\-gapsize\fR GAPSIZE
+Estimated size of gapsize in case of paired end reads,
+default = 1
+.TP
+\fB\-c\fR CUTOFF_LOWER, \fB\-\-cutoff_lower\fR CUTOFF_LOWER
+Lower cutoff: Output only reads with a score lower
+than or equal to this value, use m1 for \fB\-1\fR
+.TP
+\fB\-C\fR CUTOFF_HIGHER, \fB\-\-cutoff_higher\fR CUTOFF_HIGHER
+Higher cutoff: Output only reads with a score higher
+than or equal to this value, use m1 for \fB\-1\fR
+.TP
+\fB\-d\fR, \fB\-\-delete_temp\fR
+\eDelete temporary files. Calculations will start from
+beginning next time.
+.TP
+\fB\-f\fR FILETYPE, \fB\-\-filetype\fR FILETYPE
+Type of your input reads. fasta or fastq, default =
+fastq
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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