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commit 205ae97a2123433859102f4878227274cf7f1d3c Author: Andreas Tille <[email protected]> Date: Fri Nov 27 23:14:24 2015 +0100 Manpage --- debian/cgview.1 | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ debian/manpages | 1 + 2 files changed, 73 insertions(+) diff --git a/debian/cgview.1 b/debian/cgview.1 new file mode 100644 index 0000000..d2536c6 --- /dev/null +++ b/debian/cgview.1 @@ -0,0 +1,72 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.3. +.TH CGVIEW "1" "November 2015" "cgview 0.0.20100111" "User Commands" +.SH NAME +cgview \- Circular Genome Viewer +.SH SYNOPSIS +.B cgview +\fI[OPTIONS]\fR ... +.SH DESCRIPTION +CGView is a Java package for generating high quality, zoomable maps of +circular genomes. Its primary purpose is to serve as a component of +sequence annotation pipelines, as a means of generating visual output +suitable for the web. Feature information and rendering options are +supplied to the program using an XML file, a tab delimited file, or an +NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, +or Scalable Vector Graphics format), complete with labels, a title, +legends, and footnotes. In addition to the default full view map, the +program can generate a series of hyperlinked maps showing expanded +views. The linked maps can be explored using any web browser, allowing +rapid genome browsing, and facilitating data sharing. The feature labels +in maps can be hyperlinked to external resources, allowing CGView maps +to be integrated with existing web site content or databases. +.SH OPTIONS +.TP +\fB\-A\fR <integer> Specifies a label font size. +.TP +\fB\-c\fR <integer> Specifies the base to center on when zooming. +.TP +\fB\-D\fR <integer> Specifies a legend font size. +.TP +\fB\-d\fR <real> Specifies tick density, between 0 and 1.0. Default is 1.0. +.TP +\fB\-E\fR <boolean> Whether or not to embed vector\-based text in SVG output. +.TP +\fB\-e\fR <boolean> Whether or not to exclude SVG output from image series. +.TP +\fB\-f\fR <format> The format of the output: PNG, JPG, SVG, or SVGZ. +.TP +\fB\-h\fR <file> HTML file to create. +.TP +\fB\-H\fR <integer> The height of the map. +.TP +\fB\-i\fR <file> The input file to parse. +.TP +\fB\-I\fR <boolean> Whether or not to draw labels on the inside of the backbone circle. +.TP +\fB\-L\fR <integer> The width of an external legend. +.TP +\fB\-o\fR <file> The image file to create. +.TP +\fB\-p\fR <path> The path to the image file in the HTML file created using the \fB\-h\fR option. +.TP +\fB\-r\fR <boolean> Whether or not to remove legends. +.TP +\fB\-R\fR <boolean> Whether or not to remove labels. +.TP +\fB\-s\fR <directory> Directory to receive an image series. +.TP +\fB\-S\fR <boolean> Whether or not to reference external stylesheet in HTML output. +.TP +\fB\-u\fR <boolean> Whether or not to reference overlib.js in HTML output. +.TP +\fB\-U\fR <integer> Specifies a sequence ruler font size. +.TP +\fB\-W\fR <integer> The width of the map. +.TP +\fB\-x\fR <string> Comma separated zoom values for image series. +.TP +\fB\-z\fR <real> The factor to zoom in by. +.SH EXAMPLES +cgview \fB\-f\fR png \fB\-i\fR cybercell.xml \fB\-o\fR my_picture.png \fB\-h\fR view_image.html +.P +cgview \fB\-i\fR cybercell.xml \fB\-s\fR directory_for_series \fB\-e\fR true 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/cgview.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
