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