[med-svn] r7254 - trunk/packages/circos/trunk/debian
olivier sallou
osallou-guest at alioth.debian.org
Tue Jul 12 06:53:20 UTC 2011
Author: osallou-guest
Date: 2011-07-12 06:53:20 +0000 (Tue, 12 Jul 2011)
New Revision: 7254
Added:
trunk/packages/circos/trunk/debian/circos.1
trunk/packages/circos/trunk/debian/circos.manpages
Log:
add man page
Added: trunk/packages/circos/trunk/debian/circos.1
===================================================================
--- trunk/packages/circos/trunk/debian/circos.1 (rev 0)
+++ trunk/packages/circos/trunk/debian/circos.1 2011-07-12 06:53:20 UTC (rev 7254)
@@ -0,0 +1,279 @@
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+.\" ========================================================================
+.\"
+.IX Title "CIRCOS 1"
+.TH CIRCOS 1 "2011-07-12" "perl v5.12.4" "User Contributed Perl Documentation"
+.\" For nroff, turn off justification. Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+circos \- generate publication\-quality, circularly\-composited plots
+ of data and annotations layered on chromosome ideograms
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+.Vb 1
+\& circos \-conf circos.conf [\-silent] [\-debug] [\-help] [\-man]
+.Ve
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+This is a command line interface to Circos. Most settings are meant to be passed using a configuration file.
+.PP
+All command line options listed below can be defined in the configuration file. Defining them on the command line is useful when using a configuration template for many images.
+.SH "OPTIONS"
+.IX Header "OPTIONS"
+.SS "Configuration"
+.IX Subsection "Configuration"
+.IP "\-configfile \s-1FILE\s0" 4
+.IX Item "-configfile FILE"
+Name of configuration file. This is required.
+.SS "Ideograms"
+.IX Subsection "Ideograms"
+.IP "\-chromosomes \s-1STRING\s0" 4
+.IX Item "-chromosomes STRING"
+.PD 0
+.IP "\-chromosomes_order \s-1STRING\s0" 4
+.IX Item "-chromosomes_order STRING"
+.IP "\-chromosomes_scale \s-1STRING\s0" 4
+.IX Item "-chromosomes_scale STRING"
+.IP "\-chromosomes_radius \s-1STRING\s0" 4
+.IX Item "-chromosomes_radius STRING"
+.PD
+Defines list, order, scale and radius of ideograms.
+.SS "Output Format"
+.IX Subsection "Output Format"
+.IP "\-png" 4
+.IX Item "-png"
+.PD 0
+.IP "\-24bit" 4
+.IX Item "-24bit"
+.IP "\-svg" 4
+.IX Item "-svg"
+.PD
+Toggles output of \s-1PNG\s0 and \s-1SVG\s0 files.
+.Sp
+When using transparency, make sure that \s-1PNG\s0 output is 24\-bit.
+.SS "Output Paths"
+.IX Subsection "Output Paths"
+.IP "\-outputdir \s-1DIR\s0" 4
+.IX Item "-outputdir DIR"
+.PD 0
+.IP "\-outputfile \s-1FILE\s0" 4
+.IX Item "-outputfile FILE"
+.PD
+Change the output directory and filename.
+.SS "Input Format"
+.IX Subsection "Input Format"
+.IP "\-file_delim \s-1DELIMITER\s0" 4
+.IX Item "-file_delim DELIMITER"
+Specify the file delimiter for all input data files. By default this
+is a space. Use a tab if you want to have multi-word records in the
+data files (e.g. multi word labels).
+.SS "Custom Fields"
+.IX Subsection "Custom Fields"
+.IP "\-usertext1 \s-1STRING\s0" 4
+.IX Item "-usertext1 STRING"
+.PD 0
+.IP "\-usertext2 \s-1STRING\s0" 4
+.IX Item "-usertext2 STRING"
+.IP "\-usertext3 \s-1STRING\s0" 4
+.IX Item "-usertext3 STRING"
+.IP "\-usertext4 \s-1STRING\s0" 4
+.IX Item "-usertext4 STRING"
+.PD
+Custom fields that can be used to change any string in the
+configuration file. The fields are referenced in the configuration
+file using \f(CW\*(C`_\|_$CONF{usertext1}_\|_\*(C'\fR, etc. This is useful if you are
+creating multiple versions of an image with different settings.
+.Sp
+For example, in the configuration file you can have
+.Sp
+.Vb 2
+\& <link segdup>
+\& radius = _\|_$CONF{usertext1}_\|_r
+.Ve
+.Sp
+and then call Circos
+.Sp
+.Vb 2
+\& bin/circos ... \-usertext1 0.9
+\& bin/circos ... \-usertext1 0.5
+.Ve
+.SS "Ticks"
+.IX Subsection "Ticks"
+.IP "\-show_ticks, \-noshow_ticks" 4
+.IX Item "-show_ticks, -noshow_ticks"
+.PD 0
+.IP "\-show_tick_labels, \-noshow_tick_labels" 4
+.IX Item "-show_tick_labels, -noshow_tick_labels"
+.PD
+Toggle display of ticks and tick labels.
+.SS "Image Maps"
+.IX Subsection "Image Maps"
+.IP "\-image_map_use" 4
+.IX Item "-image_map_use"
+.PD 0
+.IP "\-image_map_name \s-1MAPNAME\s0" 4
+.IX Item "-image_map_name MAPNAME"
+.IP "\-image_map_file \s-1FILE\s0" 4
+.IX Item "-image_map_file FILE"
+.IP "\-image_map_missing_parameter { exit | removeparam | removeurl }" 4
+.IX Item "-image_map_missing_parameter { exit | removeparam | removeurl }"
+.PD
+Controls image map settings. See
+.Sp
+.Vb 1
+\& http://mkweb.bcgsc.ca/circos/tutorials/lessons/image_maps
+.Ve
+.SS "Debugging"
+.IX Subsection "Debugging"
+.IP "\-silent" 4
+.IX Item "-silent"
+Generate no reporting.
+.IP "\-verbose" 4
+.IX Item "-verbose"
+Generate verbose reporting.
+.IP "\-debug" 4
+.IX Item "-debug"
+Turn on debugging output.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Martin Krzywinski <martink at bcgsc.ca> <http://mkweb.bcgsc.ca>
+.SH "RESOURCES"
+.IX Header "RESOURCES"
+<http://mkweb.bcgsc.ca/circos>
+.SH "CITING"
+.IX Header "CITING"
+If you are using Circos in a publication, please cite as
+.PP
+Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne,
+D. Horsman, S. Jones, and M. Marra. 2009. Circos: an Information
+Aesthetic for Comparative Genomics. Genome Res 19:1639\-1645.
+.SH "CONTRIBUTORS"
+.IX Header "CONTRIBUTORS"
+Ken Youens-Clark <kyclark at gmail.com>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+Hive plots <http://www.hiveplot.com>
Added: trunk/packages/circos/trunk/debian/circos.manpages
===================================================================
--- trunk/packages/circos/trunk/debian/circos.manpages (rev 0)
+++ trunk/packages/circos/trunk/debian/circos.manpages 2011-07-12 06:53:20 UTC (rev 7254)
@@ -0,0 +1 @@
+debian/circos.1
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