Mercurial > repos > iuc > mummer_mummerplot

annotate mummerplot.xml @ 2:ebe3b0f84de9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 7ea9a5c6d9e7212c38be96baa6615af1ea9d5a8e"
author iuc
date Tue, 13 Oct 2020 21:40:53 +0000
parents c0cedc12fcc5
children 4fc0cb2ac8ae
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c0cedc12fcc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
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1 <tool id="mummer_mummerplot" name="Mummerplot" version="@MUMMER_VERSION@@WRAPPER_VERSION@">
0
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2 <description>Generate 2-D dotplot of aligned sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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c0cedc12fcc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
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7 <expand macro="gnuplot_requirement"/>
0
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8 </expand>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 ln -s $reference_sequence reference.fa &&
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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12 ln -s $query_sequence query.fa &&
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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13 mummerplot
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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14 -b '$breaklen'
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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15 $color
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16 $coverage
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17 $filter
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18 $fat
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19 #if str($labels.IDs) == 'yes':
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20 -IdR '$labels.ref_id'
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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21 -IdQ '$labels.query_id'
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22 #end if
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23 #if str($sequences.seq_input) == 'yes':
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24 -R '$reference_sequence'
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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25 -Q '$query_sequence'
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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26 $sequences.layout
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27 #end if
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28 -s '$size'
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29 -terminal png
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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30 -title '$title'
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31 $snp
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32 #if $range.custom == 'yes':
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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33 -x [$range.min_x:$range.max_x]
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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34 -y [$range.min_y:$range.max_y]
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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35 #end if
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36 '$delta'
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c0cedc12fcc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
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37 @MUMMER_GNUPLOT_MANUAL@
0
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param name="delta" type="data" format="tabular" label="Match File" />
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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42 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" />
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43 <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" />
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44 <expand macro="mumplot_input" >
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45 <conditional name="sequences" >
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46 <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
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47 <option value="no">NO</option>
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48 <option value="yes">YES</option>
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49 </param>
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50 <when value="yes">
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51 <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
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52 </when>
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53 <when value="no" />
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54 </conditional>
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55 </expand>
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56 <param name="extra_outs" type="select" label="Output files used to create the plot or just the plot?" >
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57 <option value="plot">Just the plot</option>
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58 <option value="all">All outputs</option>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data name="gnuplot" format="txt" from_work_dir="out.gp" label="${tool.name} on ${on_string}: gnuplot" >
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63 <filter> extra_outs == 'all' </filter>
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64 </data>
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65 <data name="fplot" format="txt" from_work_dir="out.fplot" label="${tool.name} on ${on_string}: fplot" >
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66 <filter> extra_outs == 'all' </filter>
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67 </data>
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68 <data name="rplot" format="txt" from_work_dir="out.rplot" label="${tool.name} on ${on_string}: rplot" >
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69 <filter> extra_outs == 'all' </filter>
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70 </data>
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71 <data name="hplot" format="txt" from_work_dir="out.hplot" label="${tool.name} on ${on_string}: hplot" >
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72 <filter> extra_outs == 'all' </filter>
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73 </data>
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74 <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" />
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75 </outputs>
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76 <tests>
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77 <test>
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78 <param name="delta" ftype="txt" value="nucmer.txt" />
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79 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
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80 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
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81 <param name="seq_input" value="no" />
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82 <param name="extra_outs" value="all" />
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83 <output name="gnuplot" ftype="txt" compare="diff" value="gnuplot.txt" />
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84 <output name="fplot" ftype="txt" compare="diff" value="fplot.txt" />
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85 <output name="rplot" ftype="txt" compare="diff" value="rplot.txt" />
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86 <output name="hplot" ftype="txt" compare="diff" value="hplot.txt" />
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87 <output name="output_png" ftype="png" compare="sim_size" value="plot.png" />
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 Mummerplot is a perl script that generates gnuplot scripts and data collections for plotting with the gnuplot utility. It can generate 2-d dotplots and 1-d coverage plots for the output of mummer or nucmer. It can also color dotplots with an identity color gradient.
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92
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93 **Outputs:**
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94 * gnuplot: The gnuplot script
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95 * fplot, rplot, hplot: The forward, reverse, and highlighted match information for plotting with gnuplot.
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96 * plot: The plotted image file
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97
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98 **Options:**::
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99
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100
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101 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
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102 sequence end
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103
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104 -color Color plot lines with a percent similarity gradient or turn off all plot color (default
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105 color by match dir) If the plot is very sparse, edit the .gp script to plot with
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106 'linespoints' instead of 'lines'
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107
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108 -c Generate a reference coverage plot (default for .tiling)
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109
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110 --filter Only display .delta alignments which represent the "best" hit to any particular spot on
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111 either sequence, i.e. a one-to-one mapping of reference and query subsequences
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112
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113 --fat Layout sequences using fattest alignment only
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114
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115 -IdR Plot a particular reference sequence ID on the X-axis
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116
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117 -IdQ Plot a particular query sequence ID on the Y-axis
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118
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119 -s Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')
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120
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121 --SNP Highlight SNP locations in each alignment
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122
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123 -title Specify the gnuplot plot title (default none)
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124
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125 -x Set the xrange for the plot '[min:max]'
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126
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127 -y Set the yrange for the plot '[min:max]'
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128
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129 -R Plot an ordered set of reference sequences from Rfile
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130
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131 -Q Plot an ordered set of query sequences from Qfile
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132
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133 --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options
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134
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135 ]]></help>
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136 <expand macro="citation" />
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137 </tool>
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138
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139
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140