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1 <tool id="CompareOverlappingSmallQuery" name="Compare Overlapping Small Query">
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2 <description>Provide the queries that overlap with a reference, when the query is small.</description>
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3 <command interpreter="python">
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4 ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1
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5 #if $formatType.FormatInputFileName1 == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName1 == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName1 == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName1 == 'gff3':
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12 -f gff3
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13 #elif $formatType.FormatInputFileName1 == 'sam':
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14 -f sam
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15 #elif $formatType.FormatInputFileName1 == 'gtf':
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16 -f gtf
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17 #end if
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18 -j $formatType2.inputFileName2
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19 #if $formatType2.FormatInputFileName2 == 'bed':
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20 -g bed
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21 #elif $formatType2.FormatInputFileName2 == 'gff':
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22 -g gff
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23 #elif $formatType2.FormatInputFileName2 == 'gff2':
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24 -g gff2
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25 #elif $formatType2.FormatInputFileName2 == 'gff3':
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26 -g gff3
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27 #elif $formatType2.FormatInputFileName2 == 'sam':
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28 -g sam
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29 #elif $formatType2.FormatInputFileName2 == 'gtf':
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30 -g gtf
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31 #end if
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32 -o $outputFileGff
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33 #if $OptionDistance.Dist == 'Yes':
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34 -d $OptionDistance.distance
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35 #end if
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11
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36 #if $OptionMinOverlap.present == 'Yes':
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37 -m $OptionMinOverlap.minOverlap
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38 #end if
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39 #if $OptionPcOverlapQuery.present == 'Yes':
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40 -p $OptionPcOverlapQuery.minOverlap
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41 #end if
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42 #if $OptionPcOverlapRef.present == 'Yes':
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43 -P $OptionPcOverlapRef.minOverlap
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44 #end if
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45 #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear':
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6
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46 -c
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11
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47 #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
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6
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48 -a
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49 #end if
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50 $InvertMatch
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51 $NotOverlapping
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11
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52 $OptionInclusionQuery
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53 $OptionInclusionRef
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6
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54 </command>
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55
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56 <inputs>
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57 <conditional name="formatType">
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58 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
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59 <option value="bed">bed</option>
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60 <option value="gff">gff</option>
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61 <option value="gff2">gff2</option>
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62 <option value="gff3">gff3</option>
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63 <option value="sam">sam</option>
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64 <option value="gtf">gtf</option>
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65 </param>
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66 <when value="bed">
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67 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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68 </when>
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69 <when value="gff">
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70 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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71 </when>
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72 <when value="gff2">
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73 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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74 </when>
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75 <when value="gff3">
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76 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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77 </when>
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78 <when value="sam">
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79 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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80 </when>
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81 <when value="gtf">
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82 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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83 </when>
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84 </conditional>
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85
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86 <conditional name="formatType2">
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87 <param name="FormatInputFileName2" type="select" label="Input Reference File Format">
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88 <option value="bed">bed</option>
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89 <option value="gff">gff</option>
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90 <option value="gff2">gff2</option>
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91 <option value="gff3">gff3</option>
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92 <option value="sam">sam</option>
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93 <option value="gtf">gtf</option>
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94 </param>
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95 <when value="bed">
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96 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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97 </when>
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98 <when value="gff">
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99 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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100 </when>
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101 <when value="gff2">
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102 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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103 </when>
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104 <when value="gff3">
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105 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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106 </when>
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107 <when value="sam">
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108 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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109 </when>
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110 <when value="gtf">
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111 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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112 </when>
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113 </conditional>
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114 <conditional name="OptionDistance">
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115 <param name="Dist" type="select" label="Maximum Distance between two reads">
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116 <option value="Yes">Yes</option>
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117 <option value="No" selected="true">No</option>
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118 </param>
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119 <when value="Yes">
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120 <param name="distance" type="integer" value="0"/>
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121 </when>
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122 <when value="No">
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123 </when>
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124 </conditional>
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11
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125 <conditional name="OptionMinOverlap">
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126 <param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap">
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127 <option value="Yes">Yes</option>
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128 <option value="No" selected="true">No</option>
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129 </param>
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130 <when value="Yes">
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131 <param name="minOverlap" type="integer" value="0"/>
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132 </when>
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133 <when value="No">
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134 </when>
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135 </conditional>
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136 <conditional name="OptionPcOverlapQuery">
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137 <param name="present" type="select" label="N% of the query must overlap">
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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="minOverlap" type="integer" value="0"/>
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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 <conditional name="OptionPcOverlapRef">
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148 <param name="present" type="select" label="N% of the reference must overlap">
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149 <option value="Yes">Yes</option>
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150 <option value="No" selected="true">No</option>
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151 </param>
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152 <when value="Yes">
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153 <param name="minOverlap" type="integer" value="0"/>
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154 </when>
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155 <when value="No">
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156 </when>
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157 </conditional>
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158 <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must nested in a query"/>
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159 <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must nested in a query"/>
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160 <conditional name="OptionCollinearOrAntiSens">
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161 <param name="OptionCA" type="select" label="Collinear or anti-sens">
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162 <option value="Collinear">Collinear</option>
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163 <option value="AntiSens">AntiSens</option>
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164 <option value="NONE" selected="true">NONE</option>
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165 </param>
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166 <when value="Collinear">
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167 </when>
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168 <when value="AntiSens">
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169 </when>
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170 <when value="NONE">
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171 </when>
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172 </conditional>
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173 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
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174 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
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175 </inputs>
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176
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177 <outputs>
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178 <data name="outputFileGff" format="gff3"/>
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179 </outputs>
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180 </tool>
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