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+++ b/MUMmer/mummerplot_tool.xml	Tue Oct 28 16:59:33 2014 +0100
@@ -0,0 +1,115 @@
+<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>
+