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1 <tool id="mummer_clustering" name="MUMmer Clustering" version="0.9.alx" force_history_refresh="True">
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2 <description>: order sequence matches in clusters</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=="gaps":
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7 $in_reference
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8 #if $tool.gaps_r=="yes":
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9 -r
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10 #end if
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11 #end if
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12 #if $tool.cmd=="mgaps":
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13 #if $tool.cmd_C=="yes":
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14 -C
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15 #end if
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16 -d $tool.cmd_d
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17 #if $tool.cmd_e=="yes":
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18 -e
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19 #end if
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20 -f $tool.cmd_f
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21 -l $tool.cmd_l
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22 -s $tool.cmd_s
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23 #end if
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24 < $tool.in_match_list
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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" 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="gaps" selected="true">gaps</option>
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32 <option value="mgaps">mgaps</option>
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33 </param>
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34 <when value="gaps">
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35 <param name="in_reference" type="data" format="fasta" label="Reference FastA file" />
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36 <param name="gaps_r" type="select" label="Use reversed [-r]" >
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37 <option value="no" selected="true">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 <param name="in_match_list" type="data" format="text" label="MUMmer match list" help="See help for more details" />
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41 </when>
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42 <when value="mgaps">
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43 <param name="in_match_list" type="data" format="text" label="MUMmer match list" help="See help for more details" />
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44 <param name="cmd_C" type="select" label="Check input header labels have reversed keyword [-C]" >
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45 <option value="no" selected="true">No</option>
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46 <option value="yes">Yes</option>
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47 </param>
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48 <param name="cmd_d" type="integer" size="5" value="5" label="Max fixed diagonal difference [-d]" />
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49 <param name="cmd_e" type="select" label="Use extent of cluster [-e]" >
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50 <option value="no" selected="true">No</option>
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51 <option value="yes">Yes</option>
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52 </param>
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53 <param name="cmd_f" type="float" size="5" value="0.05" label="Max fraction separation for diagonal difference [-f]" />
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54 <param name="cmd_l" type="integer" size="5" value="200" label="Min cluster length [-l]" />
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55 <param name="cmd_s" type="integer" size="5" value="1000" label="Max separation adjecent matches in cluster [-s]" />
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56 </when>
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57 </conditional>
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58 </inputs>
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59 <outputs>
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60 <data name="out_tool" format="text" label="Clustering output" />
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61 </outputs>
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62 <requirements>
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63 <!-- <requirement type="set_environment" version="3.23">MUMMER_PATH</requirement> -->
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64 <requirement type="package" version="4.6.4">gnuplot</requirement>
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3
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65 <requirement type="package" version="3.23">mummer</requirement>
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2
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66 </requirements>
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67 <tests>
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68 <test>
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69 </test>
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70 </tests>
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71 <help>
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72 |
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73
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74
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75 **Reference**
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76 =============
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77
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78 - **MUMmer clustering Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.
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79
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80 - **MUMmer suite v3.22:** http://mummer.sourceforge.net
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81
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82 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
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83
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84 If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve
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85 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
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86
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87
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88 **MUMmer Clustering**
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89 =====================
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90
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91 MUMmer's clustering algorithms attempt to order small individual matches into larger match clusters
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92 in order to make the output of mummer more intelligible. A dot plot makes it easy to spot alignment
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93 regions from a match list, however when examining the data without graphic aids, it is very difficult
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94 to draw any reasonable conclusions from the simple flat file list of matches. Clustering the matches
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95 together into larger groups of neighboring matches makes this process much easier by ordering the
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96 data and removing spurious matches.
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97
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98
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99 Gaps
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100 ----
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101
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102 *gaps* is the primary clustering algorithm for run-mummer1, and although classified as a "clustering"
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103 step, gaps is more of a sorting routine. It implements the LIS (longest increasing subset) algorithm
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104 to extract the longest consistent set of matches between two sequences, and generates a single
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105 cluster that represents the best "straight-line" arrangement of matches between the sequences. By
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106 straight-line, we mean no rearrangements or inversions, just a simple path of agreeing matches
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107 between the two sequences. This limits the usability of this program to the alignment of genomes
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108 that are very similar and with no large scale mutations. *gaps* is best suited for the comparison of
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109 near identical sequences with the goal of finding minor mutations like SNPs and small indels.
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110
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111 Input can be filtered mummer output. The strange syntax is a result of a legacy issue described in
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112 the Known problems (manual) section, and requires the header be stripped from the mummer output. In
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113 addition, gaps is only designed to handle a single reference and a single query sequence, thus the
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114 preceding mummer run must also follow this constraint. The -r is optional and designates the incoming
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115 matches as reverse complement matches which must reference the reverse complement of the sequence,
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116 therefore forcing mummer to be run without the -c option.
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117
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118 Reference: http://mummer.sourceforge.net/manual/#gaps
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119
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120 **Output:**
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121 ::
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122
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123 > /home/aphillip/data/GHP.1con Consistent matches
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124 183 17 22 none - -
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125 238 72 108 none 33 33
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126 347 181 92 none 1 1
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127 458 292 50 none 19 19
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128 705 539 44 none 1 1
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129 750 584 38 none 1 1
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130 807 641 23 -16 0 4
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131 (output continues ...)
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132 > Wrap around
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133 334398 329917 47 none - 225
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134 334446 329965 62 none 1 1
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135 334539 330058 20 none 31 31
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136 334560 330079 92 none 1 1
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137 334653 330172 77 none 1 1
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138 334740 330259 41 none 10 10
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139 (output continues ...)
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140 > /home/aphillip/data/GHP.1con Other matches
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141 1317231 4891 21 none - -
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142 1317275 4927 21 none - -
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143 1317804 5399 25 none 508 451
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144 947580 5436 36 none - -
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145 23406 5518 34 none - -
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146 333079 6592 32 none - -
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147 (output continues ...)
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148
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149 Where the first line is the location of the reference file, and the first three columns are the same
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150 as the three column match format described in the mummer section. The final three columns are the
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151 overlap between this match and the previous match, the gap between the start of this match and the
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152 end of the previous match in the reference, and the gap between the start of this match and the end
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153 of the previous match in the query respectively.
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154
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155
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156 mgaps
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157 -----
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158
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159 *mgaps* was introduced into the MUMmer pipeline in an effort to better handle large-scale
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160 rearrangements and duplications. Unlike gaps, mgaps is a full clustering algorithm that is capable
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161 of generating multiple groups of consistently ordered matches. Clustering is controlled by a set of
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162 command-line parameters that adjust the minimum cluster size, maximum gap between matches, etc. Only
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163 matches that were included in clusters will appear in the output, so by adjusting the command-line
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164 parameters it is possible to filter out many of the spurious matches, thus leaving only the larger
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165 areas of conservation between the input sequences. The major advantage of mgaps is its ability to
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166 identify these "islands" of conservation. This frees the user from the single LIS restraints of the
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167 gaps program and allows for the identification of large-scale rearrangements, duplications, gene
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168 families and so on.
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169
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170 Gaps can fail to identify clusters because they were not consistent with the LIS. However, by using
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171 mgaps, all regions of conservation can now been identified. The only fallback being the increased
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172 complexity of the output, where you once had only one cluster for the whole comparison, you usually
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173 now get more. Because of this, it can sometimes be difficult separating the repetitive clusters from
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174 "correct" clusters, *making mgaps more suited for global alignments instead of localized error detection*.
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175
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176 Input can be raw mummer output. *mgaps* is only designed to handle a single reference and one or
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177 more query sequences, thus the preceding mummer run must also follow this constraint. Please refer
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178 to the run-mummer3 script (see online manual) for an example of how to use this program in an
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179 alignment pipeline. Note that in order to cluster reverse complement matches, the reverse complement
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180 matches must reference the reverse complement strand of the query sequence, therefore forcing mummer
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181 to be run without the -c option. A rewrite of this algorithm to handle multiple reference sequences
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182 and a better coordinate system (forward coordinates for reverse complement matches) is doubtful but
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183 may eventually appear.
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184
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185 The -d option can be interpreted as the number of insertions allowed between two matches in the same
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186 cluster, while the -f option is a fraction equal to (diagonal difference / match separation) where
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187 a higher value will increase the indel tolerance. Minimum cluster length is the sum of the contained
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188 matches unless the -e option is used. The best way to get a feel for what each parameter controls
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189 is to cluster the same data set numerous times with different values and observe the resulting
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190 differences. It can also be helpful to set these parameters to the size of the element you wish to
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191 capture, i.e. set the minimum cluster size to say the smallest exon you expect and set the max gap
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192 to the smallest intron you expect to obtain clusters that could represent single exons (depending
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193 of course of the similarity of the two sequences).
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194
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195 Reference: http://mummer.sourceforge.net/manual/#mgaps
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196
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197 **Output format**
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198
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199 Output of *mgaps* shares much in common with the output of mummer and gaps, with a slightly different
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200 header formatting than gaps to allow for multiple query sequences and multiple clusters. The output
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201 of mgaps run on both forward and reverse complement matches is as follows:
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202 ::
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203
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204 > ID41
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205 > ID41 Reverse
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206 5177399 1 232 none - -
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207 5177632 234 6794 none 1 1
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208 5184433 7035 24 none 7 7
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209 5184468 7069 23 none 11 10
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210 > ID42
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211 10181 43 1521 none - -
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212 > ID42 Reverse
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213 4654536 17 36 none - -
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214 4654578 57 298 none 6 4
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215 4654877 356 226 none 1 1
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216 #
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217 4655139 845 28 none - -
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218 4655178 884 694 none 11 11
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219 4655873 1579 20 none 1 1
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220 #
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221 4850044 17 1492 none - -
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222 4851537 1510 711 none 1 1
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223 4852249 2222 42 none 1 1
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224 (output continues ...)
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225
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226
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227 Headers containing the ID for each query sequence are listed after the '>' characters, and a
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228 following Reverse keyword identifies the reverse matches for that query sequence. Individual clusters
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229 for each sequence are separated by a '#' character, and the six columns are exactly the same as the
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230 gaps output (see the gaps section for more details).
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231
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232
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233 |
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234 |
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235
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236 </help>
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237 </tool>
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238
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