[med-svn] [seqsero] 01/04: Add manpages

[Andreas Tille]

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tille pushed a commit to branch master
in repository seqsero.

commit 0cb42b5fee058018e7b426e4e11c29853e06a4ec
Author: Andreas Tille <tille at debian.org>
Date:   Tue Apr 4 15:25:23 2017 +0200

    Add manpages
---
 debian/manpages                 |  1 +
 debian/seqsero.1                | 27 +++++++++++++++++++++++++++
 debian/seqsero_batch_pair-end.1 | 13 +++++++++++++
 3 files changed, 41 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/seqsero.1 b/debian/seqsero.1
new file mode 100644
index 0000000..44c8205
--- /dev/null
+++ b/debian/seqsero.1
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SEQSERO "1" "April 2017" "seqsero 1.0" "User Commands"
+.SH NAME
+seqsero \- Salmonella serotyping from genome sequencing data
+.SH SYNOPSIS
+.B seqsero
+\fB\-m\fR <data_type> \fB\-i\fR <input_data> [\-b <BWA_algorithm>]
+.SH OPTIONS
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-m\fR {1,2,3,4}
+<int>: '1'(pair\-end reads, interleaved),'2'(pair\-end reads,
+seperated),'3'(single\-end reads), '4'(assembly)
+.TP
+\fB\-i\fR I [I ...]
+<string>: path/to/input_data
+.TP
+\fB\-b\fR {sam,mem}
+<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam
+.SH AUTHOR
+SeqSero was developed by Shaokang Zhang (zskzsk at uga.edu) and Xiangyu Deng (xdeng at uga.edu)
+.PP
+Contact email:seqsero at gmail.com
+.PP
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/seqsero_batch_pair-end.1 b/debian/seqsero_batch_pair-end.1
new file mode 100644
index 0000000..f5f5d10
--- /dev/null
+++ b/debian/seqsero_batch_pair-end.1
@@ -0,0 +1,13 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH SEQSERO_BATCH_PAIR-END "1" "April 2017" "seqsero_batch_pair-end 1.0" "User Commands"
+.SH NAME
+seqsero_batch_pair-end \- batch processing of paired-end reads using seqsero
+.SH SYNOPSIS
+.B seqsero_batch_pair-end
+\fI\,<dir_with_sequence_pairs>\/\fR
+.SH DESCRIPTION
+This script seeks a directory for paired\-end reads and processes
+all pairs through seqsero using \fB\-m2\fR option.  If a sequence pair
+was processed before it will be skipped.
+.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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