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1 <tool id="meme_meme" name="MEME" version="4.11.0.0">
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2 <description>- Multiple Em for Motif Elicitation</description>
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3 <requirements>
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4 <requirement type="package" version="9.07">ghostscript</requirement>
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5 <requirement type="package" version="4.11.0">meme</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 meme "$input1"
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10 -o "${html_outfile.files_path}"
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11 -nostatus
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12 #if str( $options_type.options_type_selector ) == 'advanced':
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13 -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }"
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14 -${options_type.alphabet_type.alphabet_type_selector}
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15 -mod "${options_type.mod_type.mod_type_selector}"
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16 -nmotifs "${options_type.nmotifs}"
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17 -wnsites "${options_type.wnsites}"
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18 #if $options_type.evt < float('inf'):
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19 -evt "${options_type.evt}"
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20 #end if
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21 #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
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22 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
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23 -nsites "${options_type.mod_type.motif_occurrence_type.nsites}"
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24 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
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25 -minsites "${options_type.mod_type.motif_occurrence_type.minsites}"
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26 -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"
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27 #end if
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28 #end if
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29 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
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30 -w "${options_type.motif_width_type.width}"
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31 #else
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32 -minw "${options_type.motif_width_type.minw}"
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33 -maxw "${options_type.motif_width_type.maxw}"
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34 #end if
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35 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
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36 -nomatrim
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37 #else
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38 -wg "${options_type.motif_trim_type.wg}"
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39 -ws "${options_type.motif_trim_type.ws}"
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40 ${options_type.motif_trim_type.noendgaps}
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41 #end if
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42 #if str( $options_type.bfile ) != 'None':
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43 -bfile "${options_type.bfile}"
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44 #end if
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45 #if str( $options_type.pspfile ) != 'None':
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46 -psp "${options_type.pspfile}"
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47 #end if
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48 #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":
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49 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
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50 #end if
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51 -maxiter "${options_type.maxiter}"
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52 -distance "${options_type.distance}"
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53 -prior "${options_type.alphabet_type.prior_type.prior_type_selector}"
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54 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
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55 -b "${options_type.alphabet_type.prior_type.prior_b}"
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56 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
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57 -plib "${options_type.alphabet_type.prior_type.plib}"
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58 #end if
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59 #end if
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60 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
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61 -cons "${options_type.alphabet_type.spmap_type.cons}"
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62 #else
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63 -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}"
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64 -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}"
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65 #end if
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66 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
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67 -x_branch
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68 -bfactor "${options_type.branching_type.bfactor}"
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69 -heapsize "${options_type.branching_type.heapsize}"
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70 #end if
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71 #end if
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72 2>&1 || echo "Error running MEME."
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73 && mv ${html_outfile.files_path}/meme.html ${html_outfile}
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74 && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
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75 && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
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76 ]]>
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77 </command>
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78 <inputs>
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79 <param format="fasta" name="input1" type="data" label="Sequences"/>
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80 <conditional name="options_type">
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81 <param name="options_type_selector" type="select" label="Options Configuration">
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82 <option value="basic" selected="true">Basic</option>
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83 <option value="advanced">Advanced</option>
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84 </param>
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85 <when value="basic" />
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86 <when value="advanced">
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87 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" argument="-sf"/>
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88 <conditional name="alphabet_type">
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89 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
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90 <option value="protein">Protein</option>
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91 <option value="dna" selected="true">DNA</option>
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92 </param>
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93 <when value="protein">
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94 <conditional name="prior_type">
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95 <param name="prior_type_selector" type="select" label="Choice of prior" argument="-prior">
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96 <option value="dirichlet">simple Dirichlet prior</option>
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97 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
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98 <option value="mega">extremely low variance dmix</option>
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99 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
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100 <option value="addone">add +1 to each observed count</option>
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101 </param>
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102 <when value="dirichlet">
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103 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
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104 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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105 </when>
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106 <when value="dmix">
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107 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
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108 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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109 </when>
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110 <when value="mega">
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111 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
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112 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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113 </when>
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114 <when value="megap">
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115 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
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116 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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117 </when>
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118 <when value="addone" />
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119 </conditional>
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120 <conditional name="spmap_type">
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121 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
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122 <option value="uni">uni</option>
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123 <option value="pam" selected="true">pam</option>
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124 <option value="cons">Use starting point from string</option>
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125 </param>
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126 <when value="uni">
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127 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
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128 </when>
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129 <when value="pam">
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130 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
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131 </when>
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132 <when value="cons">
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133 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
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134 </when>
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135 </conditional>
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136 </when>
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137 <when value="dna">
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138 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
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139 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
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140 <conditional name="prior_type">
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141 <param name="prior_type_selector" type="select" label="Sequence Alphabet" argument="-prior">
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142 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
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143 <option value="dmix">mixture of Dirichlets prior</option>
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144 <option value="mega">extremely low variance dmix</option>
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145 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
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146 <option value="addone">add +1 to each observed count</option>
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147 </param>
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148 <when value="dirichlet">
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149 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
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150 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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151 </when>
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152 <when value="dmix">
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153 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
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154 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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155 </when>
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156 <when value="mega">
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157 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
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158 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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159 </when>
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160 <when value="megap">
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161 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
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162 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
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163 </when>
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164 <when value="addone" />
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165 </conditional>
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166 <conditional name="spmap_type">
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167 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
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168 <option value="uni" selected="true">uni</option>
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169 <option value="pam">pam</option>
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170 <option value="cons">Use starting point from string</option>
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171 </param>
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172 <when value="uni">
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173 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
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174 </when>
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175 <when value="pam">
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176 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
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177 </when>
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178 <when value="cons">
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179 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
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180 </when>
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181 </conditional>
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182 </when>
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183 </conditional>
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184 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" />
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185 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/>
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186 <conditional name="mod_type">
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187 <param name="mod_type_selector" type="select" label="Expected motif distribution" argument="-mod">
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188 <option value="oops">One Occurrence Per Sequence</option>
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189 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
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190 <option value="anr">Any Number of Repetitions</option>
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191 </param>
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192 <when value="oops" />
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193 <when value="zoops">
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194 <conditional name="motif_occurrence_type">
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195 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
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196 <option value="default" selected="true">Use defaults</option>
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197 <option value="nsites">nsites</option>
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198 <option value="min_max_sites">min and max sites</option>
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199 </param>
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200 <when value="default" />
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201 <when value="nsites">
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202 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
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203 </when>
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204 <when value="min_max_sites">
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205 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
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206 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
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207 </when>
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208 </conditional>
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209 </when>
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210 <when value="anr">
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211 <conditional name="motif_occurrence_type">
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212 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
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213 <option value="default" selected="true">Use defaults</option>
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214 <option value="nsites">nsites</option>
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215 <option value="min_max_sites">min and max sites</option>
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216 </param>
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217 <when value="default" />
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218 <when value="nsites">
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219 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
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220 </when>
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221 <when value="min_max_sites">
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222 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
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223 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
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224 </when>
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225 </conditional>
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226 </when>
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227 </conditional>
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228 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/>
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229 <conditional name="motif_width_type">
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230 <param name="motif_width_type_selector" type="select" label="Motif width type">
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231 <option value="exact">Exact width</option>
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232 <option value="range" selected="true">Specify a range</option>
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233 </param>
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234 <when value="exact">
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235 <param name="width" type="integer" value="10" label="Width of motif to search" argument="-w"/>
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236 </when>
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237 <when value="range">
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238 <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/>
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239 <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/>
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240 </when>
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241 </conditional>
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242 <conditional name="motif_trim_type">
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243 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
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244 <option value="nomatrim">No motif trim</option>
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245 <option value="trim" selected="true">Trim motif</option>
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246 </param>
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247 <when value="nomatrim" />
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248 <when value="trim">
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249 <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/>
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250 <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/>
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251 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
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252 </when>
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253 </conditional>
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254 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" argument="-bfile"/>
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255 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/>
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256 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/>
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257 <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/>
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258 <conditional name="branching_type">
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259 <param name="branching_type_selector" type="select" label="x-branching type">
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260 <option value="x_branch">Perform x-branching</option>
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261 <option value="no_x_branch" selected="true">No x-branching</option>
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262 </param>
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263 <when value="no_x_branch" />
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264 <when value="x_branch">
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265 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/>
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266 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/>
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267 </when>
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268 </conditional>
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269 </when>
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270 </conditional>
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271 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
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272 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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273 </param>
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274 </inputs>
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275 <outputs>
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276 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
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277 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
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278 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
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279 </outputs>
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280 <tests>
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281 <test>
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282 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
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283 <param name="options_type_selector" value="basic"/>
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284 <param name="non_commercial_use" value="True"/>
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285 <output name="html_outfile" file="meme_output_html_1.html" compare="contains"/>
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286 <output name="txt_outfile" file="meme_output_txt_1.txt" lines_diff="12"/>
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287 <output name="xml_outfile" file="meme_output_xml_1.xml" lines_diff="8"/>
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288 </test>
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289 <test>
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290 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
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291 <param name="options_type_selector" value="advanced"/>
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292 <param name="plib" value="prior30.plib" ftype="txt"/>
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293 <param name="non_commercial_use" value="True"/>
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294 <output name="html_outfile" file="meme_output_html_2.html" compare="contains"/>
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295 <output name="txt_outfile" file="meme_output_txt_2.txt" lines_diff="12"/>
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296 <output name="xml_outfile" file="meme_output_xml_2.xml" lines_diff="8"/>
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297 </test>
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298 </tests>
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299 <help>
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300
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301 .. class:: warningmark
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302
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303 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
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304 Before using, be sure to review, agree, and comply with the license.**
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305
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306 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
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307
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308 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
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309 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
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310 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
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311 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
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312 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
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313 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
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314 of occurrences, and description for each motif.
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315
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316 .. class:: infomark
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317
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318 For detailed information on MEME, click here_, or view the license_.
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319
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320 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
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321 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
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322
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323 </help>
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324 <citations>
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325 <citation type="bibtex">
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326 @published{Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California,
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327 author = {Bailey,Timothy L. and Elkan, Charles},
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328 title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
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329 year = {1994},
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330 eprint = {None},
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331 url = {http://www.sdsc.edu/~tbailey/papers/ismb94.pdf}
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332 }</citation>
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333 </citations>
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334 </tool>
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