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1 <tool id="blockclust" name="BlockClust" version="0.1">
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2 <description>Non-coding RNA clustering from deep sequencing read profiles</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">blockclust</requirement>
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5
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5 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
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6 <requirement type="package" version="0.1.19 ">samtools</requirement>
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13
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7 <requirement type="package" version="1.0">blockclust_rlibs</requirement>
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9
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8 <requirement type="set_environment">BLOCKCLUST_DATA_PATH</requirement>
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4
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9 </requirements>
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10 <!--<version_command> -version</version_command>-->
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11 <command>
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12
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12 #if str($tool_mode.operation) == "pre":
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13 #set $outputdir = $tags_bed.extra_files_path
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12
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14 BlockClustPipeLine.pl -m PRE -bam $tool_mode.reads_bam -tbed $tags_bed;
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4
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15 #end if
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16
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12
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17 #if str($tool_mode.operation) == "clust":
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18 #set $outputdir = $clusters.extra_files_path
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19 #set $accept_bed=list()
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20 #set $reject_bed=list()
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21 ## prepare annotations
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12
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22 #if str($tool_mode.reference) == "hg19":
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23 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.accept.bed")
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24 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/hg19/hg19.reject.bed")
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12
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25 #elif str($tool_mode.reference) == "mm10":
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26 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.accept.bed")
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27 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/mm10/mm10.reject.bed")
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12
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28 #elif str($tool_mode.reference) == "dm3":
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29 $accept_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.accept.bed")
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30 $reject_bed.append("\$BLOCKCLUST_DATA_PATH/annotations/dm3/dm3.reject.bed")
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31 #end if
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32 BlockClustPipeLine.pl -m TEST -f SEQUENCE -c \$BLOCKCLUST_DATA_PATH/blockclust.config
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33 -t $tool_mode.input_bbo
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34 -a #echo ''.join( $accept_bed )
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35 -r #echo ''.join( $reject_bed )
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12
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36 -o $outputdir
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37 #if str($tool_mode.pred.enable_pred) == "yes":
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38 -p
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39 -pm $tool_mode.pred.pred_mode
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40 -md \$BLOCKCLUST_DATA_PATH/models
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41 -x 3;
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42 #if str($tool_mode.pred.pred_mode) == "nearest_neighbour":
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43 cp #echo os.path.join($outputdir,'nearest_neighbour_predictions.txt')# $nearest_neighbour_pred_bed;
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44 #elif str($tool_mode.pred.pred_mode) == "model_based":
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45 cp #echo os.path.join($outputdir,'model_based_predictions.txt')# $model_based_pred_bed;
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46 #end if
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47 #else:
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48 ;
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49 #end if
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50
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51 cp #echo os.path.join($outputdir, 'mcl_clusters','all_clusters.bed')# $clusters;
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52 cp #echo os.path.join($outputdir, 'hclust_tree.pdf')# $hclust_plot;
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53 cp #echo os.path.join($outputdir, 'discretized.gspan.tab')# $sim_tab_out;
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54 #end if
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55
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12
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56 #if str($tool_mode.operation) == "post":
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57 #set $outputdir = $clusters_bed.extra_files_path
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58 BlockClustPipeLine.pl -m POST -cbed $tool_mode.clusters_bed -cm $tool_mode.cmsearch_out -tab $tool_mode.sim_tab_in -o $outputdir;
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59 cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
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60 #end if
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61 </command>
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62 <inputs>
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63 <conditional name="tool_mode">
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64 <param name="operation" type="select" label="Select mode of operation">
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65 <option value="pre">Pre-processing </option>
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66 <option value="clust">Clustering</option>
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67 <option value="post">Post-processing</option>
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68 </param>
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69 <when value="pre">
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70 <param name="reads_bam" type="data" format="bam" label="BAM file containing alignments" />
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71 </when>
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72 <when value="clust">
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73 <param name="input_bbo" type="data" format="tabular" label="Input blockgroups file" />
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74 <param name="reference" type="select" label="Select reference genome">
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75 <option value="hg19">Human (hg19)</option>
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76 <option value="mm10">Mouse (mm10)</option>
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77 <option value="dm3">Fly (dm3)</option>
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78 </param>
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79 <conditional name="pred">
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80 <param name="enable_pred" type="select" label="Would you like to perform classification?">
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81 <option value="no">No</option>
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82 <option value="yes">Yes</option>
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83 </param>
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84 <when value="yes">
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85 <param name="pred_mode" type="select" label="Mode of classification">
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86 <option value="model_based">Model based</option>
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87 <option value="nearest_neighbour">Nearest neighbour</option>
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88 </param>
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89 </when>
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90 </conditional>
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91 </when>
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92 <when value="post">
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93 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" />
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94 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" />
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95 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" />
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96 </when>
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97 </conditional>
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98 </inputs>
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99
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100 <outputs>
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101 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}">
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102 <filter> tool_mode["operation"]=="pre"</filter>
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103 </data>
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104 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" >
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105 <filter> tool_mode["operation"]=="clust"</filter>
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106 </data>
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107 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}">
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108 <filter> tool_mode["operation"]=="clust"</filter>
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109 </data>
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110 <data format="bed" name="model_based_pred_bed" label="BlockClust: Model based prediction BED on ${on_string}">
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111 <filter>
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112 ((
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113 tool_mode["operation"] == 'clust' and
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114 tool_mode["pred"]["enable_pred"] == "yes" and
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115 tool_mode["pred"]["pred_mode"] == "model_based"
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116 ))
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117 </filter>
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118 </data>
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119 <data format="bed" name="nearest_neighbour_pred_bed" label="BlockClust: Nearest neighbour prediction BED on ${on_string}">
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120 <filter>
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121 ((
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122 tool_mode["operation"] == 'clust' and
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123 tool_mode["pred"]["enable_pred"] == "yes" and
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124 tool_mode["pred"]["pred_mode"] == "nearest_neighbour"
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125 ))
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126 </filter>
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127 </data>
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128 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}">
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129 <filter> tool_mode["operation"]=="clust"</filter>
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130 </data>
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131 <data format="tabular" name="analysis" label="BlockClust: Cluster analysis on ${on_string}" >
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132 <filter> tool_mode["operation"]=="post"</filter>
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133 </data>
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134 <data format="pdf" name="cluster_dist" label="BlockClust: Cluster distribution on ${on_string}" >
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135 <filter> tool_mode["operation"]=="post"</filter>
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136 </data>
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137 </outputs>
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138 <help>
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139
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140 .. class:: infomark
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141
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142 **What it does**
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143
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144 Clusters the read profiles (i.e., blockgroups) from the blockbuster tool.
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145
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146 **Inputs**
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147
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148 BlockClust needs output of tool blockbuster as input
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149
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150 **Output**
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151
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152 BlockClust produces a fasta file containing clusters.
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153
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154 ------
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155
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156 **Licenses**
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157
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158 If **BlockClust** is used to obtain results for scientific publications it
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159 should be cited as [1]_.
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160
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161 **References**
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162
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163 .. [1]
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164
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165
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166 </help>
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167 </tool>
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