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1 <tool id="mummer_utilities_tool" name="MUMmer utilities" version="0.9.alx" force_history_refresh="True">
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2 <description>: Show and filter on sequence delta file</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 $cmd_extra
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7 $input_delta
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8 #if $tool.cmd=="show-aligns":
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9 $tool.aligns1
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10 $tool.aligns2
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11 #end if
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12 > $out_tool
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13 </command>
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14 <inputs>
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15 <conditional name="tool">
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16 <param name="cmd" type="select" value="show-snps" label="MUMmer utility" help="Utilities are run with default parameters (none). For utility specific args see help below" >
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17 <option value="show-snps">show SNPs</option>
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18 <option value="show-tiling">show tiling</option>
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19 <option value="show-diff">show diff</option>
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20 <option value="show-coords">show coords</option>
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21 <option value="show-aligns">show aligns</option>
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22 <option value="delta-filter">delta filter</option>
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23 </param>
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24 <when value="show-aligns">
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25 <param name="aligns1" type="text" size="40" value="" label="IdR" help="the FastA header tag of the desired reference sequence" />
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26 <param name="aligns2" type="text" size="40" value="" label="IdQ" help="the FastA header tag of the desired query sequence" />
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27 </when>
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28 <when value="show-snps" />
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29 <when value="show-tiling" />
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30 <when value="show-coords" />
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31 <when value="show-diff" />
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32 <when value="delta-filter" />
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33 </conditional>
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34 <param name="input_delta" type="data" format="tabular" label="MUMmer delta file" />
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35 <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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36 </inputs>
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37 <outputs>
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38 <data name="out_tool" format="text" />
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39 </outputs>
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40 <requirements>
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41 <!-- <requirement type="set_environment" version="3.23">MUMMER_PATH</requirement> -->
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42 <requirement type="package" version="4.6.4">gnuplot</requirement>
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3
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43 <requirement type="package" version="3.23">mummer</requirement>
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2
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44 </requirements>
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45 <tests>
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46 <test>
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47 </test>
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48 </tests>
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49 <help>
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50 |
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51
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52
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53 **Reference**
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54 =============
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55
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56 - **MUMmer_utilities Galaxy tool wrapper:** Alex Bossers, CVI of Wageningen UR, The Netherlands.
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57
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58 - **MUMmer utilities running on MUMmer delta file:** http://mummer.sourceforge.net/manual
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59
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60 - **MUMmer tutorials:** http://mummer.sourceforge.net/examples/
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61
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62 If you found these tools/wrappers usefull in your research, please acknowledge our work. If you improve
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63 or modify the wrappers please add instead of substitute yourself into the acknowlegement section :)
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64
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65
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66 **MUMmer Utilities**
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67 ====================
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68
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69 All tools are using the MUMmer generated DELTA file! Additional arguments are only required for show-aligns.
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70
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71 Show-coords
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72 -----------
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73
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74 show-coords parses the delta alignment output of NUCmer and PROmer, and displays summary
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75 information such as position, percent identity and so on, of each alignment. It is the most
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76 commonly used tool for analyzing the delta files. *Usually the -r is used to sort lines by reference*
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77
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78
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79 Show-tiling
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80 -----------
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81
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82 show-tiling attempts to construct a tiling path out of the query contigs as mapped to the reference
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83 sequences. Given the delta alignment information of a few long reference sequences and many small
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84 query contigs, show-tiling will determine the best mapped location of each query contig. Note that
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85 each contig may only be tiled once, so repetitive regions may cause this program some difficulty.
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86 This program is useful for aiding in the scaffolding and closure of an unfinished set of contigs,
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87 if a suitable, high similarity reference genome is available. Or, if using PROmer, show-tiling will
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88 help in the identification of syntenic regions and their contig's mapping to the references.
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89
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90 This program is not suitable for "many vs. many" assembly comparisons, however a new tool based on
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91 the concepts of show-tiling should be available in the near future that will facilitate the mapping
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92 of assembly contigs.
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93
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94
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95 Show-snps
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96 ---------
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97
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98 show-snps is a utility program for reporting polymorphisms contained in a delta encoded alignment
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99 file output by NUCmer or PROmer. It catalogs all of the single nucleotide polymorphisms (SNPs) and
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100 insertions/deletions within the delta file alignments. Polymorphisms are reported one per line, in
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101 a delimited fashion similar to show-coords. Pairing this program with the appropriate MUMmer tools
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102 can create an easy to use SNP pipeline for the rapid identification of putative SNPs between any
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103 two sequence sets, as demonstrated in the manual SNP detection section.
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104
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105
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106 Show-diff
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107 ---------
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108
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109 Outputs a list of structural differences for each sequence in
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110 the reference and query, sorted by position. For a reference
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111 sequence R, and its matching query sequence Q, differences are
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112 categorized as GAP (gap between two mutually consistent alignments),
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113 DUP (inserted duplication), BRK (other inserted sequence), JMP
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114 (rearrangement), INV (rearrangement with inversion), SEQ
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115 (rearrangement with another sequence). The first five columns of
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116 the output are seq ID, feature type, feature start, feature end,
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117 and feature length. Additional columns are added depending on the
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118 feature type. Negative feature lengths indicate overlapping adjacent
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119 alignment blocks.
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120 ::
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121
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122 IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff
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123 IDR DUP dup-start dup-end dup-length
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124 IDR BRK gap-start gap-end gap-length
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125 IDR JMP gap-start gap-end gap-length
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126 IDR INV gap-start gap-end gap-length
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127 IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence
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128
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129 Positions always reference the sequence with the given ID. The
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130 sum of the fifth column (ignoring negative values) is the total
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131 amount of inserted sequence. Summing the fifth column after removing
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132 DUP features is total unique inserted sequence. Note that unaligned
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133 sequence are not counted, and could represent additional "unique"
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134 sequences. See documentation for tips on how to interpret these
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135 alignment break features.
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136
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137
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138 Show-aligns
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139 -----------
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140
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141 show-aligns parses the delta encoded alignment output of NUCmer and PROmer, and displays
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142 the pair-wise alignments from the two sequences specified on the command line. It is handy
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143 for identifying the exact location of errors and looking for SNPs between two sequences.
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144
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145
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146 Delta-filter
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147 ------------
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148
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149 delta-filter is a utility program for the manipulation of the delta encoded alignment files output
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150 by the NUCmer and PROmer pipelines. It takes a delta file as input and filters the information based
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151 on the various command line switches, outputting only the desired alignments to stdout. Options to filter by
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152 alignment length, identity, uniqueness and consistency are provided. Certain combinations of these
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153 options can greatly reduce the number of unwanted alignments in the delta file, thus making the output
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154 of programs such as show-coords more comprehendible.
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155
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156
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157
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158 **CMD line options (specific for each tool!):**
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159 ===============================================
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160
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161 **Show-coords**
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162
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163 http://mummer.sourceforge.net/manual/#coords
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164
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165 **Show-tiling**
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166
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167 http://mummer.sourceforge.net/manual/#tiling
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168
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169 **Show-snps**
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170
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171 http://mummer.sourceforge.net/manual/#snps
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172
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173 **Show-aligns**
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174
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175 http://mummer.sourceforge.net/manual/#aligns
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176
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177 **Delta-filter**
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178
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179 http://mummer.sourceforge.net/manual/#filter
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180
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181
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182 </help>
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183 </tool>
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184
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