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1 <tool id="meme_meme" name="MEME" version="1.0.0">
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2 <requirements><requirement type='package'>meme</requirement></requirements>
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3 <description>- Multiple Em for Motif Elicitation</description>
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4 <command>meme "$input1" -o "${html_outfile.files_path}"
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5 -nostatus
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6
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7 ##-p 8 ##number of processors
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8
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9 #if str( $options_type.options_type_selector ) == 'advanced':
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10 -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }"
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11 -${options_type.alphabet_type.alphabet_type_selector}
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12 -mod "${options_type.mod_type.mod_type_selector}"
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13 -nmotifs "${options_type.nmotifs}"
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14 -wnsites "${options_type.wnsites}"
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15
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16 #if $options_type.evt < float('inf'):
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17 -evt "${options_type.evt}"
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18 #end if
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19
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20 #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
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21 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
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22 -nsites "${options_type.mod_type.motif_occurrence_type.nsites}"
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23 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
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24 -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"
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25 #end if
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26 #end if
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27
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28 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
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29 -w "${options_type.motif_width_type.width}"
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30 #else
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31 -minw "${options_type.motif_width_type.minw}" -maxw "${options_type.motif_width_type.maxw}"
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32 #end if
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33
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34 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
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35 -nomatrim
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36 #else
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37 -wg "${options_type.motif_trim_type.wg}" -ws "${options_type.motif_trim_type.ws}" ${options_type.motif_trim_type.noendgaps}
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38 #end if
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39
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40 #if str( $options_type.bfile ) != 'None':
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41 -bfile "${options_type.bfile}"
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42 #end if
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43
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44 #if str( $options_type.pspfile ) != 'None':
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45 -psp "${options_type.pspfile}"
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46 #end if
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47
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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} ${options_type.alphabet_type.pal}
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50 #end if
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51
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52 -maxiter "${options_type.maxiter}" -distance "${options_type.distance}"
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53
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54 -prior "${options_type.alphabet_type.prior_type.prior_type_selector}"
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55 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
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56 -b "${options_type.alphabet_type.prior_type.prior_b}"
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57 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
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58 -plib "${options_type.alphabet_type.prior_type.plib}"
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59 #end if
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60 #end if
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61
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62 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
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63 -cons "${options_type.alphabet_type.spmap_type.cons}"
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64 #else
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65 -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}"
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66 -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}"
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67 #end if
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68
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69 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
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70 -x_branch -bfactor "${options_type.branching_type.bfactor}" -heapsize "${options_type.branching_type.heapsize}"
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71 #end if
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72
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73 ##-maxsize "1000000" ##remove hardcoded maxsize? should increase number of processors instead
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74
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75 #end if
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76
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77 2>&1 || echo "Error running MEME."
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78
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79
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80 && mv ${html_outfile.files_path}/meme.html ${html_outfile}
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81
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82 && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
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83
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84 && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
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85
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86 </command>
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87 <inputs>
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88 <param format="fasta" name="input1" type="data" label="Sequences"/>
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89
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90 <conditional name="options_type">
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91 <param name="options_type_selector" type="select" label="Options Configuration">
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92 <option value="basic" selected="true">Basic</option>
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93 <option value="advanced">Advanced</option>
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94 </param>
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95 <when value="basic">
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96 <!-- do nothing here -->
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97 </when>
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98 <when value="advanced">
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99
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100 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" />
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101
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102 <conditional name="alphabet_type">
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103 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
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104 <option value="protein">Protein</option>
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105 <option value="dna" selected="true">DNA</option>
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106 </param>
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107 <when value="protein">
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108 <conditional name="prior_type">
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109 <param name="prior_type_selector" type="select" label="Choice of prior">
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110 <option value="dirichlet">simple Dirichlet prior</option>
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111 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
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112 <option value="mega">extremely low variance dmix</option>
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113 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
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114 <option value="addone">add +1 to each observed count</option>
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115 </param>
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116 <when value="dirichlet">
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117 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
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118 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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119 </when>
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120 <when value="dmix">
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121 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
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122 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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123 </when>
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124 <when value="mega">
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125 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
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126 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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127 </when>
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128 <when value="megap">
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129 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
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130 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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131 </when>
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132 <when value="addone">
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133 <!-- no values here? -->
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134 </when>
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135 </conditional>
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136 <conditional name="spmap_type">
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137 <param name="spmap_type_selector" type="select" label="EM starting points">
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138 <option value="uni">uni</option>
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139 <option value="pam" selected="true">pam</option>
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140 <option value="cons">Use starting point from string</option>
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141 </param>
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142 <when value="uni">
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143 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
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144 </when>
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145 <when value="pam">
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146 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
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147 </when>
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148 <when value="cons">
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149 <param name="cons" type="text" value="" label="Starting point from string" />
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150 </when>
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151 </conditional>
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152 </when>
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153 <when value="dna">
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154 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
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155 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
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156 <conditional name="prior_type">
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157 <param name="prior_type_selector" type="select" label="Sequence Alphabet">
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158 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
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159 <option value="dmix">mixture of Dirichlets prior</option>
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160 <option value="mega">extremely low variance dmix</option>
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161 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
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162 <option value="addone">add +1 to each observed count</option>
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163 </param>
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164 <when value="dirichlet">
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165 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
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166 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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167 </when>
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168 <when value="dmix">
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169 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
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170 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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171 </when>
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172 <when value="mega">
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173 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
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174 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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175 </when>
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176 <when value="megap">
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177 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
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178 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
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179 </when>
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180 <when value="addone">
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181 <!-- no values here? -->
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182 </when>
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183 </conditional>
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184 <conditional name="spmap_type">
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185 <param name="spmap_type_selector" type="select" label="EM starting points">
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186 <option value="uni" selected="true">uni</option>
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187 <option value="pam">pam</option>
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188 <option value="cons">Use starting point from string</option>
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189 </param>
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190 <when value="uni">
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191 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
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192 </when>
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193 <when value="pam">
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194 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
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195 </when>
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196 <when value="cons">
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197 <param name="cons" type="text" value="" label="Starting point from string" />
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198 </when>
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199 </conditional>
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200 </when>
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201 </conditional>
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202
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203 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" />
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204 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" />
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205 <conditional name="mod_type">
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206 <param name="mod_type_selector" type="select" label="Expected motif distribution">
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207 <option value="oops">One Occurrence Per Sequence</option>
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208 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
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209 <option value="anr">Any Number of Repetitions</option>
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210 </param>
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211 <when value="oops">
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212 <!-- no values here -->
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213 </when>
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214 <when value="zoops">
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215 <conditional name="motif_occurrence_type">
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216 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
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217 <option value="default" selected="true">Use defaults</option>
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218 <option value="nsites">nsites</option>
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219 <option value="min_max_sites">min and max sites</option>
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220 </param>
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221 <when value="default">
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222 <!-- no values here -->
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223 </when>
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224 <when value="nsites">
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225 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
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226 </when>
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227 <when value="min_max_sites">
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228 <param name="minsites" type="integer" value="1" label="minsites" />
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229 <param name="maxsites" type="integer" value="50" label="maxsites" />
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230 </when>
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231 </conditional>
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232 </when>
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233 <when value="anr">
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234 <conditional name="motif_occurrence_type">
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235 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
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236 <option value="default" selected="true">Use defaults</option>
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237 <option value="nsites">nsites</option>
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238 <option value="min_max_sites">min and max sites</option>
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239 </param>
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240 <when value="default">
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241 <!-- no values here -->
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242 </when>
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243 <when value="nsites">
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244 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
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245 </when>
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246 <when value="min_max_sites">
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247 <param name="minsites" type="integer" value="1" label="minsites" />
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248 <param name="maxsites" type="integer" value="50" label="maxsites" />
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249 </when>
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250 </conditional>
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251 </when>
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252 </conditional>
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253 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" />
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254
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255 <conditional name="motif_width_type">
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256 <param name="motif_width_type_selector" type="select" label="Motif width type">
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257 <option value="exact">Exact width</option>
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258 <option value="range" selected="true">Specify a range</option>
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259 </param>
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260 <when value="exact">
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261 <param name="width" type="integer" value="10" label="Width of motif to search" />
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262 </when>
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263 <when value="range">
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264 <param name="minw" type="integer" value="8" label="Min width of motif to search" />
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265 <param name="maxw" type="integer" value="50" label="Max width of motif to search" />
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266 </when>
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267 </conditional>
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268
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269 <conditional name="motif_trim_type">
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270 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
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271 <option value="nomatrim">No motif trim</option>
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272 <option value="trim" selected="true">Trim motif</option>
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273 </param>
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274 <when value="nomatrim">
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275 <!-- no values here -->
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276 </when>
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277 <when value="trim">
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278 <param name="wg" type="integer" value="11" label="Gap cost" />
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279 <param name="ws" type="integer" value="1" label="Space cost" />
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280 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
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281 </when>
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282 </conditional>
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283
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284 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" />
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285 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" />
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286
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287 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" />
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288 <param name="distance" type="float" value="0.001" label="Convergence criterion" />
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289
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290 <conditional name="branching_type">
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291 <param name="branching_type_selector" type="select" label="x-branching type">
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292 <option value="x_branch">Perform x-branching</option>
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293 <option value="no_x_branch" selected="true">No x-branching</option>
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294 </param>
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295 <when value="no_x_branch">
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296 <!-- no values here -->
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297 </when>
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298 <when value="x_branch">
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299 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" />
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300 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" />
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301 </when>
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302 </conditional>
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303
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304 </when>
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305 </conditional>
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306
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307 <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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308 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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309 </param>
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310
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311 </inputs>
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312 <outputs>
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313 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
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314 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
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315 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
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316 </outputs>
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317 <tests>
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318 <test>
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319 <param name="input1" value="meme/meme/meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
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320 <param name="options_type_selector" value="basic"/>
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321 <param name="non_commercial_use" value="True"/>
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322 <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/>
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323 <output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/>
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324 <output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/>
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325 </test>
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326 </tests>
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327 <help>
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328
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329 .. class:: warningmark
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330
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331 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.**
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332
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333 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
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334
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335 .. class:: infomark
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336
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337 **To cite MEME:**
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338 Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
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339
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340
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341 For detailed information on MEME, click here_. To view the license_.
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342
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343 ------
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344
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345 **Citation**
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346
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347 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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348
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349 .. _here: http://meme.nbcr.net/meme/meme-intro.html
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350 .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
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351
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352 </help>
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353 </tool>
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