Commit 81ce6af4 authored by Andreas Tille's avatar Andreas Tille

Add manpage using help2man output

parent 160c7070
help2man --no-info --help-option=" " --no-discard-stderr \
--name='Integrating PSMs Into Genome browser visualizations' \
--version-string="2012-06-19" ipig > debian/ipig.1
.TH IPIG "1" "February 2014" "ipig 2012-06-19" "User Commands"
ipig \- Integrating PSMs Into Genome browser visualizations
.B ipig
\fI<psm file>\fR |\-g|\-c|\-cg [<config file>]
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 (
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.
\fI<psm file>\fR
indicates the file with the
peptide spectrum matches (mzid/txt)
\fB\-g\fR, \fB\-gui\fR
starts the graphical user interface of iPiG
\fB\-c\fR, \fB\-control\fR
starts the gene control, necessary files have
to be indicated in the configuration file
\fB\-cg\fR, \fB\-controlgui\fR
starts the graphical user interface of the gene control
\fB\-d\fR, \fB\-downloader\fR
starts the download gui
<config file>
a different configuration file can be indicated
(otherwise ipig.conf is loaded by default)
additional requirements:
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.
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.
have a look into readme.txt and ipig.conf for examples and
more details about the additional parameters
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