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1 <tool id="mummer_maxmatch" name="MUMmer MaxMatch" version="0.9.alx" force_history_refresh="True">
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2 <description>: Maximal exact sequence matching</description>
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3 <command>
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4 <!-- update this path to the installed location -->
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5 $tool.cmd
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6 #if $tool.cmd=="mummer":
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7 $tool.cmd_extra
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8 $tool.mum_ref_in
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9 $tool.mum_q_in
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10 #end if
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11 #if $tool.cmd=="repeat-match":
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12 -n $tool.rm_n
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13 #if $tool.rm_E=="yes":
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14 -E
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15 #end if
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16 $tool.cmd_extra
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17 $tool.in_seq
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18 #end if
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19 #if $tool.cmd=="exact-tandems":
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20 $tool.in_seq
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21 $tool.et_minl
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22 #end if
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23 <!-- unfortunate somehow error state gets set also on succesfull jobs. Pipe io stderr to dev/null -->
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24 2>&-
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25 > $out_tool
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26
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27 </command>
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28 <inputs>
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29 <conditional name="tool">
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30 <param name="cmd" type="select" value="mummer" label="MUMmer maximal matching" help="Algorithms are run with default parameters (none). For specific args see help below" >
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31 <option value="mummer">mummer</option>
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32 <option value="repeat-match">repeat-match</option>
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33 <option value="exact-tandems">exact-tandems</option>
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34 </param>
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35 <when value="mummer">
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36 <param name="mum_ref_in" type="data" format="fasta" label="Reference FastA file" />
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37 <param name="mum_q_in" type="data" format="fasta" label="Query (multi) FastA sequence" />
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38 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="See specific cmd line options below for each tool" />
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39 </when>
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40 <when value="repeat-match">
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41 <param name="in_seq" type="data" format="fasta" label="FastA sequence file" />
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42 <param name="rm_n" type="text" size="5" value="20" label="Minimum exact match length [-n]" />
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43 <param name="rm_E" type="select" value="no" label="Use exhaustive (slow) search to find matches [-E]" >
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44 <option value="no">No</option>
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45 <option value="yes">Yes</option>
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46 </param>
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47 <param name="cmd_extra" type="text" size="40" value="" label="Extra cmd line options" help="-n and -E are configured above. More specific cmd line options in help below." />
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48 </when>
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49 <when value="exact-tandems">
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50 <param name="in_seq" type="data" format="fasta" label="FastA sequence file" />
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51 <param name="et_minl" type="text" size="5" value="20" label="Minimum length" />
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52 </when>
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53 </conditional>
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54 </inputs>
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55 <outputs>
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56 <data name="out_tool" format="text" label="Max exact match output" />
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57 </outputs>
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58 <requirements>
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59 <!-- <requirement type="set_environment" version="3.23">MUMMER_PATH</requirement> -->
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60 <requirement type="package" version="4.6.4">gnuplot</requirement>
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61 <requirement type="package" version="3.23">MUMmer</requirement>
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62 </requirements>
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63 <tests>
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64 <test>
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65 </test>
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66 </tests>
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67 <help>
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68 |
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69
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70
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71 **Reference**
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72 =============
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73
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74 - **MUMmer MaxExactMatch Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.
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75
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76 - **MUMmer suite v3.22:** http://mummer.sourceforge.net
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77
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78 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
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79
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80 Please do not use any of the command line options that modify prefixes or file names. As obvious
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81 they are quite useless within galaxy and are likely to fail the routine!
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82
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83 If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve
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84 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
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85
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86
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87
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88 **MUMmer Maximal exact matching**
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89 =================================
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90
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91 The heart of the MUMmer package is its suffix tree based maximal matching routines. These can be
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92 used for repeat detection within a single sequence as is done by *repeat-match* and *exact-tandems*,
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93 or can be used for the alignment of two or more sequences as is done by *mummer*.
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94
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95 Mummer
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96 ------
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97
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98 mummer is a suffix tree algorithm designed to find maximal exact matches of some minimum length
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99 between two input sequences. by default mummer will only find maximal matches that are unique in
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100 the entire set of reference sequences. The match lists produced by mummer can be used alone to
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101 generate alignment dot plots, or can be passed on to the clustering algorithms for the identification
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102 of longer non-exact regions of conservation. These match lists have great versatility because they
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103 contain huge amounts of information and can be passed forward to other interpretation programs for
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104 clustering, analysis, searching, etc.
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105
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106
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107 Repeat-match
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108 ------------
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109
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110 repeat-match is a suffix tree algorithm designed to find maximal exact repeats within a single input
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111 sequence. It uses a similar algorithm to mummer, but altered slightly to find maximal exact matches
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112 within a single sequence.
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113
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114 Output formatting varies depending on the command line parameters and the output can be quite large.
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115 The standard output format that results from running repeat-match with default parameters is as follows:
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116 ::
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117
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118 Long Exact Matches:
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119 Start1 Start2 Length
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120 4919485 4919506r 22
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121
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122 The three columns are the first position of the repeat, the second position of the repeat, and the
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123 length of the repeat respectively. Reverse complement repeat positions are denoted by an 'r'
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124 following the Start2 position, and are relative to the forward strand of the sequence.
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125
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126
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127 Exact-tandems
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128 -------------
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129
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130 exact-tandems is a wrapper script for the repeat-match program. It provides a list of exact tandem
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131 repeats within a single input sequence. As with repeat-match the sequence file should contain only
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132 one sequence in FastA format, however if multiple sequences exist the first one will be used. The
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133 sequence may contain any set of upper and lowercase characters, thus DNA and protein sequence are
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134 both allowed and matching is case insensitive. The minimum match length parameter should be a
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135 positive integer, this value will be passed to the repeat-match program via the -n option.
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136
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137 The output format of exact-tandems is as follows:
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138 ::
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139
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140 Finding matches
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141 Tandem repeats
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142 Start Extent UnitLen Copies
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143 416173 150 45 3.3
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144
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145 The four columns are the first position of the tandem, the extent of the repeat region, the length
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146 of each tandem repeat unit, and the number of repeat units respectively.
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147
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148
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149
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150 **Manuals and CMD line options (specific for each tool!):**
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151 ===========================================================
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152
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153 **Mummer**
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154
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155 http://mummer.sourceforge.net/manual/#mummer
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156
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157 **Repeat-match**
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158
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159 http://mummer.sourceforge.net/manual/#repeat
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160
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161 **exact-tandems**
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162
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163 http://mummer.sourceforge.net/manual/#exact
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164
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165 |
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166 |
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167
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168 </help>
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169 </tool>
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170
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