<tool id="mummerplot_tool" name="MUMmer plot" version="1.0.1" force_history_refresh="true">
  <description>: Generate MUMmerplots from MUMmer match file</description>
  <command interpreter="bash">
  		mummerplot_tool.sh 
		#if $img_format=="png": 
			png $input_match $out_png
		#else: 
			postscript $input_match $out_postscript
		#end if
		$cmd_extra
  </command>
	<inputs>
		<param name="input_match" type="data" format="tabular" label="MUMmer match (delta or tiling) file" />
		<!-- <conditional name="outType"> -->
			<param name="img_format" type="select" label="Output format" >
				<option value="png" selected="true">PNG image</option>
				<option value="postscript">Postscript</option>
			</param>
		<!--  </conditional>  -->
		<param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="See cmd line options below" />
	</inputs>
	<outputs>
		<data name="out_png" format="png" label="MUMmerplot png">
			<filter>img_format=="png"</filter>
		</data>
		<data name="out_postscript" format="ps" label="MUMmerplot ps">
			<filter>img_format=="postscript"</filter>
		</data>
	</outputs>
    <requirements>
<!--         <requirement type="set_environment" version="3.23">MUMMER_PATH</requirement> -->
        <requirement type="package" version="4.6.4">gnuplot</requirement>
        <requirement type="package" version="3.23">mummer</requirement>
    </requirements>
	<tests>
		<test>
		</test>
	</tests>
	<help>
|


**Reference**
=============
 
- **MUMmerplot Galaxy tool wrapper: Alex Bossers, CVI of Wageningen UR, The Netherlands**

- **MUMmerplot running on MUMmer-match file:** http://mummer.sourceforge.net/manual#mummerplot

- **MUMmer tutorials:** http://mummer.sourceforge.net/examples/

If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve 
or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)


**MUMmerplot**
==============

| This plotting tool requires a MUMmer match file (either the delta file or the tiling result file)! 
| MUMmerplot requires gnuplot (www.gnuplot.info) to be installed. 
| 
| **The plotting has by default set the arguments --large and --png/--postscript to generate a fixed image instead of an interactive view!** Optional cmd line arguments can be used.
| 



Mummerplot is a script utility that takes output from *MUMmer, nucmer or promer* as DELTA file, or the 
*show-tiling* result file, and converts it to a format suitable for plotting with gnuplot. The primary 
plot type is an alignment dotplot where a sequence is laid out on each axis and a point is plotted at 
every position where the two sequences show similarity. As an extension to this plot style, mummerplot 
is also able to offset multiple 1-vs-1 dotplots to form a multiplot where multiple sequences can be 
laid out on each axis. This plot style is especially handy for browsing an alignment of two contig 
sets. Identity plots are also possible by coloring each data point with a color gradient representing 
identity, or by collapsing the y-axis data onto a single line and then vertically offsetting the 
data points by their identities. In addition to producing the plot data, mummerplot also generates a 
gnuplot script that will be evaluated in order to generate the graph.


The *match file* can either be a three column match list from mummer (either 3 or 4 column format), 
the delta file from nucmer or promer, or the default output from show-tiling. mummerplot will 
automatically detect the type of input file it is given, regardless of its file extension, or it 
will fail if the input file is of an unrecognized type. 



Optional command line arguments
-------------------------------

--breaklen  Highlight alignments with a breakpoint further than the given distance from the nearest sequence end 
--nocolor  Color plot lines with a percent similarity gradient or turn off all color (default color by match direction) 
--coverage  Generate a reference coverage plot, also known as a percent identity plot (default behavior for show-tiling input) 
--depend  Print dependency information and exit 
--filter  Only display alignments which represent the "best" one-to-one mapping of reference and query subsequences (requires delta formatted input) 
--help  Print help information and exit 
--layout  Layout a multiplot by ordering and orienting sequences such that the largest hits cluster near the main diagonal (requires delta formatted input)  
--prefix  *do not use in galaxy!* Set the output file prefix (default 'out') 
--rv  Reverse video, swap the foreground and background colors for x11 plots (requires x11 terminal) 
--IdR  Select a specific reference sequence for the x-axis 
--IdQ  Select a specific query sequence for the y-axis 
--Rfile  Generate a multiplot by using the order and length information contained in this file, either a FastA file of the desired reference sequences or a tab-delimited list of sequence IDs, lengths and orientations [ +-] 
--Qfile  Generate a multiplot by using the order and length information contained in this file, either a FastA file of the desired query sequences or a tab-delimited list of sequence IDs, lengths and orientations [ +-] 
--size  Set the output size to small, medium or large
--large  **default enabled to generate highres image**. Other sizes no effect: --small  --medium --large
--SNP  Highlight SNP locations in the alignment 
--terminal  *do not use in galaxy* Set the output terminal to x11, postscript or png
--png  **either png or postscript for fixed image**. Other interactive x11 not enabled 
--postscript  Alternate output format instead of png. 
--xrange  Set the x-range for the plot in the form "[min,max]" 
--yrange  Set the y-range for the plot in the form "[min,max]" 
--version  Display version information and exit 


	</help>
</tool>