[med-svn] [sspace] 04/08: add man page

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

sascha-guest pushed a commit to branch master
in repository sspace.

commit 38c33bebed42e8b8e16a5c64beeb777cbe14e7bb
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Tue Jun 7 21:33:49 2016 +0000

    add man page
---
 debian/control       |  4 ++-
 debian/manpages      |  1 +
 debian/rules         |  7 +++++
 debian/sspace.1.adoc | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 93 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index fc8bb7d..6932be1 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,9 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               recode
+               recode,
+               python,
+               asciidoctor
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sspace.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/sspace.git
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..f52cc9b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/sspace.1
diff --git a/debian/rules b/debian/rules
index 91b7b89..8c54dc0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,7 +5,14 @@
 %:
 	dh $@
 
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -f debian/sspace.1
+
 override_dh_install:
 	dh_install
 	find debian -name "*.pl" -exec recode ibmpc.. \{\} \;
 
+override_dh_installman:
+	asciidoctor -a docdate='' -b manpage debian/sspace.1.adoc
+	dh_installman
diff --git a/debian/sspace.1.adoc b/debian/sspace.1.adoc
new file mode 100644
index 0000000..7d1de48
--- /dev/null
+++ b/debian/sspace.1.adoc
@@ -0,0 +1,82 @@
+# sspace(1)
+
+## NAME
+
+sspace - SSPACE-basic scaffolding tool
+
+## SYNOPSIS
+
+*sspace* [options] -l [libraryfilename]  -s [contigfilename]
+
+## DESCRIPTION
+
+SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired-end libraries, or even a combination.
+
+Please read the README file at /usr/share/doc/sspace/README.gz for more information.
+
+## OPTIONS
+
+### General Parameters
+
+  *-l*::
+  Library file containing two paired read files with insert size, error and either mate pair or paired end indication (REQUIRED)
+
+  *-s*::
+  FASTA file containing contig sequences used for extension. Inserted pairs are mapped to extended and non-extended contigs (REQUIRED)
+
+  *-x*::
+  Indicate whether to extend the contigs of -s using paired reads in -l (-x 1=extension, -x 0=no extension, default -x 0)
+
+### Extension Parameters
+
+  *-m*::
+  Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 32)
+
+  *-o*::
+  Minimum number of reads needed to call a base during an extension (default -o 20)
+
+  *-t*::
+  Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)
+
+  *-u*::
+  FASTA/FASTQ file containing unpaired sequence reads (optional)
+
+  *-r*::
+  Minimum base ratio used to accept a overhang consensus base (default -r 0.9)
+
+### Scaffolding Parameters
+
+  *-z*::
+  Minimum contig length used for scaffolding. Filters out contigs below this value (default -z 0)
+
+  *-k*::
+  Minimum number of links (read pairs) to compute scaffold (default -k 5)
+
+  *-a*::
+  Maximum link ratio between two best contig pairs. *Higher values lead to least accurate scaffolding* (default -a 0.7)
+
+  *-n*::
+  Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -n 15)
+
+### Bowtie Parameters
+
+  *-g*::
+  Maximum number of allowed gaps during mapping with Bowtie. Corresponds to the -v option in Bowtie. Higher number of allowed gaps can lead to least accurate scaffolding. (default -g 0)
+
+  *-T*::
+  Specify the number of threads in Bowtie. Corresponds to the -p/--threads option in Bowtie (default -T 1)
+
+### Additional Parameters
+
+  *-b*::
+  Base name for your output files (default -b standard_output)
+
+  *-v*::
+  Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0)
+
+  *-p*::
+  Make .dot file for visualisation (-p 1=yes, -p 0=no, default -p 0)
+
+## AUTHORS
+
+Marten Boetzer, Walter Pirovano, Nicola Soranzo

-- 
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