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comparison MUMmer/mummerplot_tool.xml @ 2:479eb076cd23

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Add revised mummer toolshed files to testtoolshed
author abossers
date Tue, 28 Oct 2014 16:59:33 +0100
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1 <tool id="mummerplot_tool" name="MUMmer plot" version="1.0.1" force_history_refresh="true">
2 <description>: Generate MUMmerplots from MUMmer match file</description>
3 <command interpreter="bash">
4 mummerplot_tool.sh
5 #if $img_format=="png":
6 png $input_match $out_png
7 #else:
8 postscript $input_match $out_postscript
9 #end if
10 $cmd_extra
11 </command>
12 <inputs>
13 <param name="input_match" type="data" format="tabular" label="MUMmer match (delta or tiling) file" />
14 <!-- <conditional name="outType"> -->
15 <param name="img_format" type="select" label="Output format" >
16 <option value="png" selected="true">PNG image</option>
17 <option value="postscript">Postscript</option>
18 </param>
19 <!-- </conditional> -->
20 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="See cmd line options below" />
21 </inputs>
22 <outputs>
23 <data name="out_png" format="png" label="MUMmerplot png">
24 <filter>img_format=="png"</filter>
25 </data>
26 <data name="out_postscript" format="ps" label="MUMmerplot ps">
27 <filter>img_format=="postscript"</filter>
28 </data>
29 </outputs>
30 <requirements>
31 <!-- <requirement type="set_environment" version="3.23">MUMMER_PATH</requirement> -->
32 <requirement type="package" version="4.6.4">gnuplot</requirement>
33 <requirement type="package" version="3.23">MUMmer</requirement>
34 </requirements>
35 <tests>
36 <test>
37 </test>
38 </tests>
39 <help>
40 |
41
42
43 **Reference**
44 =============
45
46 - **MUMmerplot Galaxy tool wrapper: Alex Bossers, CVI of Wageningen UR, The Netherlands**
47
48 - **MUMmerplot running on MUMmer-match file:** http://mummer.sourceforge.net/manual#mummerplot
49
50 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
51
52 If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve
53 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
54
55
56 **MUMmerplot**
57 ==============
58
59 | This plotting tool requires a MUMmer match file (either the delta file or the tiling result file)!
60 | MUMmerplot requires gnuplot (www.gnuplot.info) to be installed.
61 |
62 | **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.
63 |
64
65
66
67 Mummerplot is a script utility that takes output from *MUMmer, nucmer or promer* as DELTA file, or the
68 *show-tiling* result file, and converts it to a format suitable for plotting with gnuplot. The primary
69 plot type is an alignment dotplot where a sequence is laid out on each axis and a point is plotted at
70 every position where the two sequences show similarity. As an extension to this plot style, mummerplot
71 is also able to offset multiple 1-vs-1 dotplots to form a multiplot where multiple sequences can be
72 laid out on each axis. This plot style is especially handy for browsing an alignment of two contig
73 sets. Identity plots are also possible by coloring each data point with a color gradient representing
74 identity, or by collapsing the y-axis data onto a single line and then vertically offsetting the
75 data points by their identities. In addition to producing the plot data, mummerplot also generates a
76 gnuplot script that will be evaluated in order to generate the graph.
77
78
79 The *match file* can either be a three column match list from mummer (either 3 or 4 column format),
80 the delta file from nucmer or promer, or the default output from show-tiling. mummerplot will
81 automatically detect the type of input file it is given, regardless of its file extension, or it
82 will fail if the input file is of an unrecognized type.
83
84
85
86 Optional command line arguments
87 -------------------------------
88
89 --breaklen Highlight alignments with a breakpoint further than the given distance from the nearest sequence end
90 --nocolor Color plot lines with a percent similarity gradient or turn off all color (default color by match direction)
91 --coverage Generate a reference coverage plot, also known as a percent identity plot (default behavior for show-tiling input)
92 --depend Print dependency information and exit
93 --filter Only display alignments which represent the "best" one-to-one mapping of reference and query subsequences (requires delta formatted input)
94 --help Print help information and exit
95 --layout Layout a multiplot by ordering and orienting sequences such that the largest hits cluster near the main diagonal (requires delta formatted input)
96 --prefix *do not use in galaxy!* Set the output file prefix (default 'out')
97 --rv Reverse video, swap the foreground and background colors for x11 plots (requires x11 terminal)
98 --IdR Select a specific reference sequence for the x-axis
99 --IdQ Select a specific query sequence for the y-axis
100 --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 [ +-]
101 --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 [ +-]
102 --size Set the output size to small, medium or large
103 --large **default enabled to generate highres image**. Other sizes no effect: --small --medium --large
104 --SNP Highlight SNP locations in the alignment
105 --terminal *do not use in galaxy* Set the output terminal to x11, postscript or png
106 --png **either png or postscript for fixed image**. Other interactive x11 not enabled
107 --postscript Alternate output format instead of png.
108 --xrange Set the x-range for the plot in the form "[min,max]"
109 --yrange Set the y-range for the plot in the form "[min,max]"
110 --version Display version information and exit
111
112
113 </help>
114 </tool>
115