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1 <tool id="interElementGff" name="interElementGff">
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2 <description>Creates a new Gff output, which corresponds to the region of two successive Elements. </description>
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3 <command interpreter="perl">
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4 interElementGff.pl -i $inputFile
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5
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6 #if $Optionf5ff.option == "Yes":
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7 -f5ff $Optionf5ff.f5ffValue
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8 #end if
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9
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10 #if $Optionff3f.option == "Yes":
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11 -ff3f $Optionff3f.ff3fValue
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12 #end if
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13
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14 #if $Optionf5fr.option == "Yes":
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15 -f5fr $Optionf5fr.f5frValue
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16 #end if
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17
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18 #if $Optionff3r.option == "Yes":
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19 -ff3r $Optionff3r.ff3rValue
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20 #end if
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21
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22 #if $Optionf3rf.option == "Yes":
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23 -f3rf $Optionf3rf.f3rfValue
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24 #end if
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25
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26 #if $Optionfr5f.option == "Yes":
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27 -fr5f $Optionfr5f.fr5fValue
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28 #end if
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29
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30 #if $Optionf3rr.option == "Yes":
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31 -f3rr $Optionf3rr.f3rrValue
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32 #end if
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33
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34 #if $Optionfr5r.option == "Yes":
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35 -fr5r $Optionfr5r.fr5rValue
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36 #end if
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37
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38 #if $Optionr5ff.option == "Yes":
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39 -r5ff $Optionr5ff.r5ffValue
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40 #end if
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41
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42 #if $Optionrf3f.option == "Yes":
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43 -rf3f $Optionrf3f.rf3fValue
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44 #end if
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45
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46 #if $Optionr5fr.option == "Yes":
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47 -r5fr $Optionr5fr.r5frValue
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48 #end if
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49
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50 #if $Optionrf3r.option == "Yes":
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51 -rf3r $Optionrf3r.rf3rValue
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52 #end if
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53
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54 #if $Optionr3rf.option == "Yes":
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55 -r3rf $Optionr3rf.r3rfValue
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56 #end if
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57
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58 #if $Optionrr5f.option == "Yes":
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59 -rr5f $Optionrr5f.rr5fValue
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60 #end if
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61
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62 #if $Optionr3rr.option == "Yes":
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63 -r3rr $Optionr3rr.r3rrValue
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64 #end if
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65
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66 #if $Optionrr5r.option == "Yes":
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67 -rr5r $Optionrr5r.rr5rValue
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68 #end if
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69
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70 -o $outputFile
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71 </command>
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72
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73 <inputs>
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74 <param name="inputFile" type="data" label="Input File" format="gff"/>
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75
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76 <conditional name="Optionf5ff">
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77 <param name="option" type="select" label="Option[f5ff]" help="number of nt to exclude from 5' seed when gene before is Forward, seed is Forward and next gene is Forward [default 0]">
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78 <option value="Yes">Yes</option>
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79 <option value="No" selected="true">No</option>
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80 </param>
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81 <when value="Yes">
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82 <param name="f5ffValue" type="integer" value="10"/>
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83 </when>
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84 <when value="No">
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85 </when>
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86 </conditional>
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87
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88 <conditional name="Optionff3f">
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89 <param name="option" type="select" label="Option[ff3f]">
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90 <option value="Yes">Yes</option>
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91 <option value="No" selected="true">No</option>
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92 </param>
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93 <when value="Yes">
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94 <param name="ff3fValue" type="integer" value="30"/>
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95 </when>
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96 <when value="No">
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97 </when>
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98 </conditional>
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99
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100 <conditional name="Optionf5fr">
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101 <param name="option" type="select" label="Option[f5fr]">
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102 <option value="Yes">Yes</option>
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103 <option value="No" selected="true">No</option>
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104 </param>
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105 <when value="Yes">
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106 <param name="f5frValue" type="integer" value="10"/>
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107 </when>
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108 <when value="No">
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109 </when>
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110 </conditional>
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111
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112 <conditional name="Optionff3r">
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113 <param name="option" type="select" label="Option[ff3r]">
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114 <option value="Yes">Yes</option>
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115 <option value="No" selected="true">No</option>
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116 </param>
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117 <when value="Yes">
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118 <param name="ff3rValue" type="integer" value="-10"/>
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119 </when>
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120 <when value="No">
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121 </when>
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122 </conditional>
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123
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124 <conditional name="Optionf3rf">
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125 <param name="option" type="select" label="Option[f3rf]">
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126 <option value="Yes">Yes</option>
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127 <option value="No" selected="true">No</option>
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128 </param>
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129 <when value="Yes">
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130 <param name="f3rfValue" type="integer" value="-10"/>
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131 </when>
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132 <when value="No">
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133 </when>
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134 </conditional>
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135
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136 <conditional name="Optionfr5f">
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137 <param name="option" type="select" label="Option[fr5f]">
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138 <option value="Yes">Yes</option>
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139 <option value="No" selected="true">No</option>
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140 </param>
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141 <when value="Yes">
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142 <param name="fr5fValue" type="integer" value="10"/>
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143 </when>
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144 <when value="No">
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145 </when>
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146 </conditional>
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147
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148 <conditional name="Optionf3rr">
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149 <param name="option" type="select" label="Option[f3rr]">
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150 <option value="Yes">Yes</option>
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151 <option value="No" selected="true">No</option>
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152 </param>
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153 <when value="Yes">
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154 <param name="f3rrValue" type="integer" value="-10"/>
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155 </when>
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156 <when value="No">
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157 </when>
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158 </conditional>
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159
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160 <conditional name="Optionfr5r">
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161 <param name="option" type="select" label="Option[fr5r]">
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162 <option value="Yes">Yes</option>
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163 <option value="No" selected="true">No</option>
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164 </param>
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165 <when value="Yes">
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166 <param name="fr5rValue" type="integer" value="10"/>
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167 </when>
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168 <when value="No">
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169 </when>
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170 </conditional>
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171
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172 <conditional name="Optionr5ff">
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173 <param name="option" type="select" label="Option[r5ff]">
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174 <option value="Yes">Yes</option>
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175 <option value="No" selected="true">No</option>
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176 </param>
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177 <when value="Yes">
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178 <param name="r5ffValue" type="integer" value="10"/>
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179 </when>
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180 <when value="No">
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181 </when>
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182 </conditional>
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183
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184 <conditional name="Optionrf3f">
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185 <param name="option" type="select" label="Option[rf3f]">
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186 <option value="Yes">Yes</option>
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187 <option value="No" selected="true">No</option>
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188 </param>
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189 <when value="Yes">
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190 <param name="rf3fValue" type="integer" value="30"/>
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191 </when>
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192 <when value="No">
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193 </when>
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194 </conditional>
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195
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196 <conditional name="Optionr5fr">
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197 <param name="option" type="select" label="Option[r5fr]">
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198 <option value="Yes">Yes</option>
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199 <option value="No" selected="true">No</option>
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200 </param>
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201 <when value="Yes">
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202 <param name="r5frValue" type="integer" value="10"/>
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203 </when>
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204 <when value="No">
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205 </when>
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206 </conditional>
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207
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208 <conditional name="Optionrf3r">
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209 <param name="option" type="select" label="Option[rf3r]">
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210 <option value="Yes">Yes</option>
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211 <option value="No" selected="true">No</option>
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212 </param>
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213 <when value="Yes">
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214 <param name="rf3rValue" type="integer" value="-10"/>
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215 </when>
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216 <when value="No">
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217 </when>
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218 </conditional>
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219
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220 <conditional name="Optionr3rf">
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221 <param name="option" type="select" label="Option[r3rf]">
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222 <option value="Yes">Yes</option>
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223 <option value="No" selected="true">No</option>
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224 </param>
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225 <when value="Yes">
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226 <param name="r3rfValue" type="integer" value="30"/>
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227 </when>
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228 <when value="No">
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229 </when>
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230 </conditional>
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231
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232 <conditional name="Optionrr5f">
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233 <param name="option" type="select" label="Option[rr5f]">
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234 <option value="Yes">Yes</option>
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235 <option value="No" selected="true">No</option>
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236 </param>
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237 <when value="Yes">
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238 <param name="rr5fValue" type="integer" value="10"/>
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239 </when>
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240 <when value="No">
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241 </when>
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242 </conditional>
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243
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244 <conditional name="Optionr3rr">
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245 <param name="option" type="select" label="Option[r3rr]">
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246 <option value="Yes">Yes</option>
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247 <option value="No" selected="true">No</option>
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248 </param>
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249 <when value="Yes">
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250 <param name="r3rrValue" type="integer" value="30"/>
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251 </when>
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252 <when value="No">
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253 </when>
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254 </conditional>
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255
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256 <conditional name="Optionrr5r">
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257 <param name="option" type="select" label="Option[rr5r]">
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258 <option value="Yes">Yes</option>
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259 <option value="No" selected="true">No</option>
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260 </param>
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261 <when value="Yes">
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262 <param name="rr5rValue" type="integer" value="10"/>
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263 </when>
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264 <when value="No">
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265 </when>
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266 </conditional>
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267
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268 </inputs>
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269
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270 <outputs>
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271 <data name="outputFile" format="gff" label="[interElementGff] Output File"/>
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272 </outputs>
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273
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274 <help>
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275 command example: interElementGff.pl -i ${i}_annot.gff -o ${i}_trans_IG.gff -f5ff 10 -ff3f 30 -f5fr 10 -ff3r -10 -f3rf -10 -fr5f 10 -f3rr -10 -fr5r 10 -r5ff 10 -rf3f 30 -r5fr 10 -rf3r -10 -r3rf 30 -rr5f 10 -r3rr 30 -rr5r 10
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276 </help>
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277
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278 </tool>
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279
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280
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281
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282
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283
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284
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