Mercurial > repos > iuc > mummer_nucmer

annotate nucmer.xml @ 4:7cd7a55a678d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
author iuc
date Mon, 18 Mar 2024 12:41:25 +0000
parents e18267f90096
children
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e18267f90096 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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1 <tool id="mummer_nucmer" name="Nucmer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>Align two or more sequences</description>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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3 <macros>
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4 <import>macros.xml</import>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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5 </macros>
3
e18267f90096 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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6 <expand macro="bio_tools"/>
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a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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7 <expand macro="requirements">
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8 <expand macro="gnuplot_requirement"/>
0
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9 </expand>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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10 <command detect_errors="exit_code">
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11 <![CDATA[
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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12 ln -s $reference_sequence reference.fa &&
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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13 ln -s $query_sequence query.fa &&
4
7cd7a55a678d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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14 nucmer
0
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15 $anchoring
4
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16 #if $outform.out_format != "delta":
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17 --sam-long=outsam.sam
7cd7a55a678d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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18 #end if
0
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19 -b '$breaklen'
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20 -c '$mincluster'
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21 -D '$diagdiff'
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22 -d '$diagfactor'
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23 $noextend
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24 $direction
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25 -g '$maxgap'
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26 -l '$minmatch'
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27 -L '$minalign'
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28 $nooptimize
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29 $nosimplify
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30 --threads "\${GALAXY_SLOTS:-1}"
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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31 #if $options.advanced == 'enable':
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32 $options.banded
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33 $options.large
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34 $options.genome
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35 -M '$options.max_chunk'
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36 #end if
4
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37 'reference.fa' 'query.fa'
7cd7a55a678d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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38 #if $outform.out_format == "delta":
7cd7a55a678d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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39 #if $mumplot.plot == 'yes' :
0
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40 && mummerplot
4
7cd7a55a678d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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41 #if $outform.mumplot.sequences.seq_input == 'yes':
0
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42 -R '$reference_sequence'
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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43 -Q '$query_sequence'
4
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44 $outform.mumplot.sequences.layout
0
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45 #end if
4
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46 -b '$outform.mumplot.breaklen'
7cd7a55a678d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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47 $outform.mumplot.color
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48 $outform.mumplot.coverage
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49 $outform.mumplot.filter
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50 $outform.mumplot.fat
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51 #if $outform.mumplot.labels.IDs == 'yes':
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52 -IdR '$outform.mumplot.labels.ref_id'
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53 -IdQ '$outform.mumplot.labels.query_id'
0
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54 #end if
4
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55 -s '$outform.mumplot.size'
0
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56 -terminal png
4
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57 -title '$outform.mumplot.title'
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58 $outform.mumplot.snp
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59 #if $outform.mumplot.range.custom == 'yes':
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60 -x [$outform.mumplot.range.min_x:$outform.mumplot.range.max_x]
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61 -y [$outform.mumplot.range.min_y:$outform.mumplot.range.max_y]
0
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62 #end if
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63 'out.delta'
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64 @MUMMER_GNUPLOT_MANUAL@
4
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65 #end if
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66 #else:
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67 && samtools dict reference.fa > outsamhead
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68 && tail -n +3 outsam.sam >> outsamhead
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69 && samtools sort -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" outsamhead |
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70 #if $outform.out_format == 'bam-long':
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71 samtools calmd -b --threads {GALAXY_SLOTS:-1} - reference.fa > outsam
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72 #else if $outform.out_format == 'cram-long':
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73 samtools view -C --reference reference.fa -o outsam -
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74 #end if
0
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75 #end if
1
5b0b49b5421c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
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76 ]]>
4
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77 </command>
0
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78 <inputs>
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79 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
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80 <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
4
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81 <conditional name="outform">
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82 <param name="out_format" type="select" label="Output format" help="Select delta format if a plot is needed. Jbrowse is a good choice to view cram and bam tracks">
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83 <option value="bam-long">bam format</option>
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84 <option value="cram-long">cram format</option>
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85 <option value="delta">Mummer delta format - allows plots</option>
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86 </param>
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87 <when value="delta">
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88 <conditional name="mumplot" >
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89 <param name="plot" type="select" label="Create a 2-D dotplot of the input sequences?" >
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90 <option value="no">No plot</option>
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91 <option value="yes">Plot</option>
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92 </param>
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93 <when value="yes" >
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94 <expand macro="mumplot_input" >
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95 <conditional name="sequences" >
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96 <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
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97 <option value="no">NO</option>
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98 <option value="yes">YES</option>
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99 </param>
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100 <when value="yes">
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101 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="(-R)" />
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102 <param name="query_sequence" type="data" format="fasta" multiple="True" label="Query Sequence(s)" help="(-Q)" />
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103 <param argument="--layout" type="boolean" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion." />
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104 </when>
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105 <when value="no" />
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106 </conditional>
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107 </expand>
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108 </when>
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109 <when value="no" />
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110 </conditional>
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111 </when>
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112 <when value="bam-long"/>
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113 <when value="cram-long"/>
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114 </conditional>
0
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115 <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
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116 <option value="">Use default</option>
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117 <option value="--mum">Unique matches only (--mum)</option>
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118 <option value="--maxmatch">All matches (--maxmatch)</option>
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119 </param>
4
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120
0
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121 <param name="breaklen" type="integer" argument="-b" value="200" label="Break Length"
4
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122 help="Set the distance an alignment extension will attempt to extend poor scoring regions before giving up." />
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123 <param name="mincluster" type="integer" argument="-c" value="65" label="Minumum Cluster Length" help="Sets the minimum length of a cluster of matches." />
0
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124 <param name="diagdiff" type="integer" argument="-D" value="5" label="Maximum Diagonal Difference"
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125 help="Set the maximum diagonal difference between two adjacent anchors in a cluster." />
0
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126 <param name="diagfactor" type="float" argument="-d" value="0.12" label="Maximum Diagonal Difference"
4
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127 help="Set the maximum diagonal difference between two adjacent anchors in a cluster as a differential fraction of the gap length." />
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128 <param type="boolean" argument="--noextend" truevalue="--noextend" falsevalue="" label="No Extend" help="Do not perform cluster extension step." />
0
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129 <param name="direction" type="select" label="Direction" help="Choose a direction of Query Sequence to Use">
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130 <option value="">Use forward and reverse sequences</option>
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131 <option value="-f">Use only forward sequence of query (-f)</option>
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132 <option value="-r">Use only reverse sequence of query (-r)</option>
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133 </param>
4
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134 <param name="maxgap" type="integer" argument="-g" value="90" label="Maximum Gap Distance" help="Set the maximum gap between two adjacent matches in a cluster." />
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135 <param name="minmatch" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Set the minimum length of a single exact match." />
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136 <param name="minalign" type="integer" argument="-L" value="0" label="Minumum Alignment Length" help="Minimum length of an alignment, after clustering and extension." />
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137 <param type="boolean" argument="--nooptimize" truevalue="--nooptimize" falsevalue="" label="No Alignment Score Optimization"
0
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138 help="No alignment score optimization, i.e. if an alignment extension reaches the end of a sequence, it will not backtrack to optimize the alignment score and instead terminate the alignment at the end of the sequence. (--nooptimize)" />
4
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139 <param type="boolean" argument="--nosimplify" truevalue="--nosimplify" falsevalue="" label="Don't Simplify Alignments"
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140 help="Don't simplify alignments by removing shadowed clusters. Use this option when aligning a sequence to itself to look for repeats." />
0
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141 <conditional name="options">
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142 <param name="advanced" type="select" label="Additional options">
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143 <option value="defaults">Use defaults</option>
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144 <option value="enable">Select additional options</option>
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145 </param>
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146 <when value="enable">
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147 <param type="boolean" argument="--banded" truevalue="--banded" falsevalue="" label="Banding"
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148 help="Enforce absolute banding of dynamic programming matrix based on diagdiff parameter. (--banded)" />
4
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149 <param type="boolean" argument="--large" truevalue="--large" falsevalue="" label="Offsets" help="Force the use of large offsets. (--large)" />
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150 <param name="genome" type="boolean" argument="-G" truevalue="-G" falsevalue="" label="Map genome to genome" help="For long query sequences. (-G)" />
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151 <param name="max_chunk" type="integer" argument="-M" value="50000" label="Max Chunk" help="Stop adding sequence for a thread if more than MAX already. (-M)" />
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152 </when>
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153 <when value="defaults" />
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154 </conditional>
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155 </inputs>
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156 <outputs>
4
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157 <data name="delta_output" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta format">
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158 <filter>outform["out_format"] == "delta"</filter>
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159 </data>
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160 <data name="sam_output" format="bam" from_work_dir="outsam" label="${tool.name} on ${on_string}">
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161 <filter>outform["out_format"] != "delta"</filter>
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162 <change_format>
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163 <when input="outform.out_format" value="cram-long" format="cram" />
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164 </change_format>
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165 </data>
0
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166 <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
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167 <filter>outform["out_format"] == "delta" and outform['mumplot']['plot'] == 'yes'</filter>
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168 </data>
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169 </outputs>
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170 <tests>
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171 <test expect_num_outputs="2">
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172 <param name="advanced" value="defaults" />
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173 <conditional name="outform">
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174 <param name="out_format" value="delta" />
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175 </conditional>
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176 <param name="plot" value="yes" />
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177 <param name="seq_input" value="yes" />
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178 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
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179 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
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180 <output name="delta_output" ftype="tabular" compare="diff" lines_diff="2" value="nucmer.txt"/>
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181 <output name="png_output" ftype="png" compare="sim_size" value="plot.png" />
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182 </test>
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183 <test expect_num_outputs="1">
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184 <param name="advanced" value="defaults" />
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185 <conditional name="outform">
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186 <param name="out_format" value="bam-long" />
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187 </conditional>
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188 <param name="seq_input" value="yes" />
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189 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
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190 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
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191 <output name="sam_output" ftype="bam" compare="sim_size" value="out.bam" />
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192 </test>
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193 <test expect_num_outputs="1">
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194 <param name="advanced" value="defaults" />
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195 <conditional name="outform">
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196 <param name="out_format" value="cram-long" />
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197 </conditional>
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198 <param name="seq_input" value="yes" />
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199 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta"/>
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200 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
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201 <output name="sam_output" ftype="cram" compare="sim_size" value="out.cram" />
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202 </test>
0
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203 </tests>
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204 <help><![CDATA[
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205 nucmer is for the all-vs-all comparison of nucleotide sequences contained in multi-FastA data files. It is best used for highly similar sequence that may
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206 have large rearrangements. Common use cases are: comparing two unfinished shotgun sequencing assemblies, mapping an unfinished sequencing assembly
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207 to a finished genome, and comparing two fairly similar genomes that may have large rearrangements and duplications.
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208
4
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209 All output coordinates reference the forward strand of the involved sequence, regardless of the match direction. Also, nucmer now uses only matches that
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210 are unique in the reference sequence by default, use different Anchoring options to change this behavior.
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211
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212 **Options:**::
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213
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214 Defaults in parentheses
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215
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216 nucmer
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217
4
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218 --sam-long The original output format of nucmer, the delta format, contains only the minimum information necessary to quickly recreate the alignment.
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219 It contains the name of the matching sequences, the length of the match, number of errors and positions of indels.
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220 With --sam-long, it additionally reports the MD string (which specifies the mismatching positions), the sequence and, if applicable,
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221 the quality values of the matching sequence. The long format is more expensive to compute and it generates larger output files,
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222 but this option allows nucmer4 to match the behavior of other aligners such as Bowtie2 or BWA.
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223
0
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224 --mum Use anchor matches that are unique in both the reference and query (false)
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225
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226 --maxmatch Use all anchor matches regardless of their uniqueness (false)
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227
4
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228 -b Set the distance an alignment extension will attempt to extend poor scoring regions
0
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229 before giving up (200)
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230
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231 -c Sets the minimum length of a cluster of matches (65)
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232
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233 -D Set the maximum diagonal difference between two adjacent anchors in a cluster (5)
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234
4
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235 -d Set the maximum diagonal difference between two adjacent anchors in a cluster as a
0
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236 differential fraction of the gap length (0.12)
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237
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238 --noextend Do not perform cluster extension step (false)
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239
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240 -f Use only the forward strand of the Query sequences (false)
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241
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242 -r Use only the reverse complement of the Query sequences (false)
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243
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244 -g Set the maximum gap between two adjacent matches in a cluster (90)
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245
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246 -l Set the minimum length of a single exact match (20)
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247
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248 -L Minimum length of an alignment, after clustering and extension (0)
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249
4
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250 --nooptimize No alignment score optimization, i.e. if an alignment extension reaches the end of a
0
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251 sequence, it will not backtrack to optimize the alignment score and instead terminate
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252 the alignment at the end of the sequence (false)
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253
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254 --nosimplify Don't simplify alignments by removing shadowed clusters. Use this option when aligning
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255 a sequence to itself to look for repeats (false)
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256
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257 --banded Enforce absolute banding of dynamic programming matrix based on diagdiff parameter (false)
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258
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259 --large Force the use of large offsets (false)
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260
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261 -G Map genome to genome (long query sequences) (false)
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262
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263 -M Max chunk. Stop adding sequence for a thread if more than MAX already. (50000)
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264
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265 mummerplot
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266
4
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267 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
0
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268 sequence end
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269
4
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270 -color Color plot lines with a percent similarity gradient or turn off all plot color (default
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271 color by match dir) If the plot is very sparse, edit the .gp script to plot with
0
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272 'linespoints' instead of 'lines'
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273
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274 -c Generate a reference coverage plot (default for .tiling)
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275
4
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276 --filter Only display .delta alignments which represent the "best" hit to any particular spot on
0
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277 either sequence, i.e. a one-to-one mapping of reference and query subsequences
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278
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279 --fat Layout sequences using fattest alignment only
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280
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281 -IdR Plot a particular reference sequence ID on the X-axis
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282
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283 -IdQ Plot a particular query sequence ID on the Y-axis
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284
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285 -s Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')
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286
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287 --SNP Highlight SNP locations in each alignment
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288
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289 -title Specify the gnuplot plot title (default none)
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290
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291 -x Set the xrange for the plot '[min:max]'
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292
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293 -y Set the yrange for the plot '[min:max]'
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294
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295 -R Plot an ordered set of reference sequences from Rfile
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296
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297 -Q Plot an ordered set of query sequences from Qfile
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298
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299 --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options
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300
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301 ]]></help>
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302 <expand macro="citation" />
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303 </tool>