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1 <?xml version="1.0"?>
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2 <toolbox>
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3 <section name="Get Data" id="getext">
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4 <tool file="data_source/upload.xml"/>
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5 </section>
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6 <section name="Text Manipulation" id="textutil">
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7 <tool file="filters/fixedValueColumn.xml" />
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8 <tool file="stats/column_maker.xml" />
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9 <tool file="filters/catWrapper.xml" />
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10 <tool file="filters/cutWrapper.xml" />
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11 <tool file="filters/mergeCols.xml" />
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12 <tool file="filters/convert_characters.xml" />
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13 <tool file="filters/CreateInterval.xml" />
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14 <tool file="filters/cutWrapper.xml" />
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15 <tool file="filters/changeCase.xml" />
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16 <tool file="filters/pasteWrapper.xml" />
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17 <tool file="filters/remove_beginning.xml" />
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18 <tool file="filters/randomlines.xml" />
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19 <tool file="filters/headWrapper.xml" />
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20 <tool file="filters/tailWrapper.xml" />
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21 <tool file="filters/trimmer.xml" />
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22 <tool file="filters/wc_gnu.xml" />
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23 <tool file="filters/secure_hash_message_digest.xml" />
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24 <tool file="stats/dna_filtering.xml" />
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25 <tool file="new_operations/tables_arithmetic_operations.xml" />
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26 </section>
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27 <section name="Filter and Sort" id="filter">
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28 <tool file="stats/filtering.xml" />
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29 <tool file="filters/sorter.xml" />
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30 <tool file="filters/grep.xml" />
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31
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32 <label text="GFF" id="gff" />
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33 <tool file="filters/gff/extract_GFF_Features.xml" />
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34 <tool file="filters/gff/gff_filter_by_attribute.xml" />
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35 <tool file="filters/gff/gff_filter_by_feature_count.xml" />
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36 <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
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37 </section>
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38 <section name="Join, Subtract and Group" id="group">
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39 <tool file="filters/joiner.xml" />
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40 <tool file="filters/compare.xml"/>
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41 <tool file="new_operations/subtract_query.xml"/>
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42 <tool file="stats/grouping.xml" />
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43 <tool file="new_operations/column_join.xml" />
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44 </section>
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45 <section name="Convert Formats" id="convert">
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46 <tool file="filters/axt_to_concat_fasta.xml" />
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47 <tool file="filters/axt_to_fasta.xml" />
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48 <tool file="filters/axt_to_lav.xml" />
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49 <tool file="filters/bed2gff.xml" />
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50 <tool file="fasta_tools/fasta_to_tabular.xml" />
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51 <tool file="filters/gff2bed.xml" />
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52 <tool file="filters/lav_to_bed.xml" />
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53 <tool file="maf/maf_to_bed.xml" />
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54 <tool file="maf/maf_to_interval.xml" />
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55 <tool file="maf/maf_to_fasta.xml" />
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56 <tool file="fasta_tools/tabular_to_fasta.xml" />
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57 <tool file="fastq/fastq_to_fasta.xml" />
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58 <tool file="filters/wiggle_to_simple.xml" />
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59 <tool file="filters/sff_extractor.xml" />
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60 <tool file="filters/gtf2bedgraph.xml" />
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61 <tool file="filters/wig_to_bigwig.xml" />
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62 <tool file="filters/bed_to_bigbed.xml" />
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63 </section>
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64
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65 <section name="Statistics" id="stats">
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66 <tool file="stats/gsummary.xml" />
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67 <tool file="filters/uniq.xml" />
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68 <tool file="stats/cor.xml" />
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69 <tool file="stats/generate_matrix_for_pca_lda.xml" />
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70 <tool file="stats/lda_analy.xml" />
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71 <tool file="stats/plot_from_lda.xml" />
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72 <tool file="regVariation/t_test_two_samples.xml" />
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73 <tool file="regVariation/compute_q_values.xml" />
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74 <tool file="stats/MINE.xml" />
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75
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76 <label text="GFF" id="gff" />
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77 <tool file="stats/count_gff_features.xml" />
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78 </section>
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79 <section name="Graph/Display Data" id="plots">
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80 <tool file="plotting/histogram2.xml" />
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81 <tool file="plotting/scatterplot.xml" />
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82 <tool file="plotting/bar_chart.xml" />
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83 <tool file="plotting/xy_plot.xml" />
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84 <tool file="plotting/boxplot.xml" />
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85 <tool file="visualization/GMAJ.xml" />
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86 <tool file="visualization/LAJ.xml" />
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87 <tool file="visualization/build_ucsc_custom_track.xml" />
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88 <tool file="maf/vcf_to_maf_customtrack.xml" />
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89 <tool file="mutation/visualize.xml" />
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90 </section>
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91 <section name="Multiple regression" id="multReg">
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92 <tool file="regVariation/linear_regression.xml" />
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93 <tool file="regVariation/logistic_regression_vif.xml" />
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94 <tool file="regVariation/best_regression_subsets.xml" />
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95 <tool file="regVariation/rcve.xml" />
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96 <tool file="regVariation/partialR_square.xml" />
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97 </section>
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98 <section name="Multivariate Analysis" id="multVar">
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99 <tool file="multivariate_stats/pca.xml" />
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100 <tool file="multivariate_stats/cca.xml" />
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101 <tool file="multivariate_stats/kpca.xml" />
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102 <tool file="multivariate_stats/kcca.xml" />
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103 </section>
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104
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105 <!--
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106 This is the MPDS 1.0.1 modules
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107 -->
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108 <label text="MPDS 1.0.1" id="mpds" />
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109 <section name="Module1_2_4 (Search Target Compound Fragment Library)" id="mpdssearch">
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110 <tool file="module_mpds_databases/mpdssearch.xml"/>
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111 </section>
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112 <section name="Module1 (Target Library)" id="tlib">
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113 </section>
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114 <section name="Module2 (Compound Library)" id="clib">
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115 </section>
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116 <section name="Module3 (File-Format Convertor)" id="ffc">
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117 <tool file="CADDSuite/galaxyconfigs/tools/Converter.xml" />
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118 </section>
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119 <section name="Module4 (Fragment Library)" id="flib">
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120 </section>
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121 <section name="Module5 (Descriptor Calculation)" id="disp">
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122 <!-- tool file="cdk/cdk.xml"/ -->
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123 <tool file="admetpred/cdk.xml"/>
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124 </section>
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125 <section name="Deepak (Descriptor Calculation)" id="dis">
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126 <tool file="cdk/cdk.xml"/>
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127 <tool file="PaDEL/padel.xml"/>
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128 </section>
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129
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130 <section name="Module6 (QSAR)" id="qsar">
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131 <tool file="mcqsar/mcqsar.xml"/>
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132 <tool file="mcqsar/mcqsar_prediction.xml"/>
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133 </section>
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134 <section name="Module7 (Docking)" id="docking_prgram">
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135 <tool file="Docking/receptor_pdbqt.xml"/>
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136 </section>
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137 <section name="Module8 (Filters)" id="filt">
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138 <tool file="admetpredictor/descal.xml"/>
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139 <tool file="admetpredictor/DruLiTo.xml"/>
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140 <tool file="admetpredictor/Split1.xml"/>
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141 <tool file="admetpredictor/BCSclass.xml" />
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142 </section>
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143 <section name="Module9 (Visualization)" id="visu">
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144 <tool file="module9/view3d.xml"/>
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145 </section>
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146 <!--
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147 <section name="Module1 Docking (using Autodock)" id="autodock">
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148 <tool file="autodock/receptor_pdbqt.xml"/>
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149 </section>
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150 <section name="Module2: Descriptor Processing" id="module2">
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151 <tool file="module2/upload.xml"/>
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152 <tool file="filters/convert_characters.xml" />
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153 <tool file="module2/2d_to_3d.xml"/>
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154 <tool file="module2/desc_calc.xml"/>
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155 <tool file="module2/filtering.xml"/>
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156 <tool file="module2/inputqsar.xml"/>
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157 <tool file="module2/view3d.xml"/>
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158 </section>
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159 <section name="module3 Database Library" id="module3">
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160 </section>
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161 <section name="Module4 Build Predictive Model" id="pmodel">
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162 <tool file="pmodel/tool1.xml" />
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163 <tool file="pmodel/tool2.xml" />
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164 <tool file="pmodel/tool3.xml" />
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165 </section>
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166 <section name="Module5 admetpred" id="admetpred">
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167 <tool file="admetpred/upload.xml"/>
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168 <tool file="admetpred/descal.xml"/>
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169 <tool file="admetpred/dlf.xml"/>
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170 <tool file="admetpred/split1.xml"/>
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171 <tool file="admetpred/cdk.xml"/>
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172 <tool file="admetpred/metapred.xml"/>
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173 </section>
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174 <section name="Module6 Docking Results Analysis Tools" id="drat">
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175 <tool file="drat/filter1.xml" />
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176 <tool file="drat/filter2.xml" />
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177 <tool file="drat/plotligplot.xml" />
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178 </section>
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179 -->
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180
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181 </toolbox>
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