[med-svn] [ipig] 01/01: Add manpage using help2man output

[Andreas Tille]

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

tille pushed a commit to branch master
in repository ipig.

commit 81ce6af46c3e2c05fcdc0a4c7c29ad08cbfdda62
Author: Andreas Tille <tille at debian.org>
Date:   Mon Feb 10 10:24:47 2014 +0100

    Add manpage using help2man output
---
 debian/createmanpages |  3 +++
 debian/ipig.1         | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/manpages       |  1 +
 3 files changed, 54 insertions(+)

diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..fa6488b
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,3 @@
+help2man --no-info --help-option=" " --no-discard-stderr \
+         --name='Integrating PSMs Into Genome browser visualizations' \
+            --version-string="2012-06-19" ipig > debian/ipig.1
diff --git a/debian/ipig.1 b/debian/ipig.1
new file mode 100644
index 0000000..8eead9d
--- /dev/null
+++ b/debian/ipig.1
@@ -0,0 +1,50 @@
+.TH IPIG "1" "February 2014" "ipig 2012-06-19" "User Commands"
+.SH NAME
+ipig \- Integrating PSMs Into Genome browser visualizations
+.SH SYNOPSIS
+.B ipig
+\fI<psm file>\fR |\-g|\-c|\-cg [<config file>]
+.SH DESCRIPTION
+.P
+iPiG targets the integration of peptide spectrum matches (PSMs) from
+mass spectrometry (MS) peptide identifications into genomic
+visualisations provided by genome browser such as the UCSC genome
+browser (http://genome.ucsc.edu/).
+.P
+iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in
+text format and provides results in genome track formats (BED and GFF3
+files), which can be easily imported into genome browsers.
+.SH OPTIONS
+.TP
+\fI<psm file>\fR
+indicates the file with the
+peptide spectrum matches (mzid/txt) 
+.TP
+\fB\-g\fR, \fB\-gui\fR
+starts the graphical user interface of iPiG
+.TP
+\fB\-c\fR, \fB\-control\fR
+starts the gene control, necessary files have
+to be indicated in the configuration file
+.TP
+\fB\-cg\fR, \fB\-controlgui\fR
+starts the graphical user interface of the gene control
+.TP
+\fB\-d\fR, \fB\-downloader\fR
+starts the download gui
+.TP
+<config file>
+a different configuration file can be indicated
+(otherwise ipig.conf is loaded by default)
+.PP
+        
+additional requirements:
+.IP
+using a non\-gui mode, a config file (ipig.conf by default) has to contain
+several additional parameters, e.g. indicating the reference genome etc.
+.IP
+in a gui mode (\fB\-g\fR and \fB\-cg\fR), additional parameters can be indicated two ways,
+within the interface or with a config file as well.
+.IP
+have a look into readme.txt and ipig.conf for examples and
+more details about the additional parameters
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

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ipig.git