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1 <tool id="CompareOverlapping_parallel" name="CompareOverlapping (for DEA)">
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2 <description>Shrink or extend the sets of genomic coordinates to get the information between starts of reads and starts of genes.</description>
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3 <command interpreter="python">
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4 compareOverlapping_parallel.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
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19 --inputTxt $inputTxt
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20
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21 -g $format2
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22
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23 --outTxt $outTxtFile
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24
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25 #if $optionNFirstFile1.NFirstForFile1 == 'Yes':
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26 -S $optionNFirstFile1.firstNtFile1
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27 #end if
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28 #if $optionNFirstFile2.NFirstForFile2 == 'Yes':
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29 -s $optionNFirstFile2.firstNtFile2
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30 #end if
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31 #if $optionNLastFile1.NLastForFile1 == 'Yes':
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32 -U $optionNLastFile1.lastNtFile1
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33 #end if
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34 #if $optionNLastFile2.NLastForFile2 == 'Yes':
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35 -u $optionNLastFile2.lastNtFile2
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36 #end if
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37
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38 #if $optionExtentionCinqFile1.extentionFile1 == 'Yes':
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39 -E $optionExtentionCinqFile1.extention51
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40 #end if
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41 #if $optionExtentionCinqFile2.extentionFile2 == 'Yes':
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42 -e $optionExtentionCinqFile2.extention52
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43 #end if
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44
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45 #if $optionExtentionTroisFile1.extentionFile1 == 'Yes':
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46 -N $optionExtentionTroisFile1.extention31
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47 #end if
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48 #if $optionExtentionTroisFile2.extentionFile2 == 'Yes':
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49 -n $optionExtentionTroisFile2.extention32
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50 #end if
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51
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52 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
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53 -c
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54 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
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55 -a
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56 #end if
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57
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58 #if $OptionDistance.Dist == 'Yes':
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59 -d $OptionDistance.distance
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60 #end if
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61
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62 #if $OptionMinOverlap.MO == 'Yes':
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63 -m $OptionMinOverlap.minOverlap
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64 #end if
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65
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66 $InvertMatch
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67 $ReportIntron
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68 $NotOverlapping
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69 $tar $outputTarFile
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70 </command>
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71
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72 <inputs>
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73
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74 <conditional name="formatType">
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75 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
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76 <option value="bed">bed</option>
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77 <option value="gff">gff</option>
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78 <option value="gff2">gff2</option>
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79 <option value="gff3">gff3</option>
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80 <option value="sam">sam</option>
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81 <option value="gtf">gtf</option>
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82 </param>
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83 <when value="bed">
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84 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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85 </when>
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86 <when value="gff">
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87 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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88 </when>
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89 <when value="gff2">
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90 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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91 </when>
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92 <when value="gff3">
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93 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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94 </when>
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95 <when value="sam">
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96 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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97 </when>
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98 <when value="gtf">
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99 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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100 </when>
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101 </conditional>
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102
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103 <param name="inputTxt" type="data" format="txt" label="A txt file contains a list of several input transcripts files." />
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104
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105 <param name="format2" type="text" value="bed" label="format for File 2, you can choose [bed, gff, gff2, gff3, sam, gtf]"/>
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106
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107 <conditional name="optionNFirstFile1">
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108 <param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">
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109 <option value="Yes">Yes</option>
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110 <option value="No" selected="true">No</option>
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111 </param>
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112 <when value="Yes">
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113 <param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />
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114 </when>
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115 <when value="No">
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116 </when>
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117 </conditional>
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118 <conditional name="optionNFirstFile2">
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119 <param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2">
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120 <option value="Yes">Yes</option>
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121 <option value="No" selected="true">No</option>
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122 </param>
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123 <when value="Yes">
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124 <param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" />
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125 </when>
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126 <when value="No">
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127 </when>
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128 </conditional>
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129
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130 <conditional name="optionNLastFile1">
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131 <param name="NLastForFile1" type="select" label="NLast for file 1">
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132 <option value="Yes">Yes</option>
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133 <option value="No" selected="true">No</option>
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134 </param>
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135 <when value="Yes">
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136 <param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/>
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137 </when>
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138 <when value="No">
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139 </when>
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140 </conditional>
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141 <conditional name="optionNLastFile2">
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142 <param name="NLastForFile2" type="select" label="NLast for file 2">
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143 <option value="Yes">Yes</option>
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144 <option value="No" selected="true">No</option>
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145 </param>
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146 <when value="Yes">
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147 <param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>
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148 </when>
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149 <when value="No">
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150 </when>
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151 </conditional>
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152
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153 <conditional name="optionExtentionCinqFile1">
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154 <param name="extentionFile1" type="select" label="Extension towards 5 for file 1">
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155 <option value="Yes">Yes</option>
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156 <option value="No" selected="true">No</option>
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157 </param>
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158 <when value="Yes">
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159 <param name="extention51" type="integer" value="1" label="in file 1" />
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160 </when>
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161 <when value="No">
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162 </when>
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163 </conditional>
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164
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165 <conditional name="optionExtentionCinqFile2">
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166 <param name="extentionFile2" type="select" label="Extension towards 5 for file 2">
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167 <option value="Yes">Yes</option>
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168 <option value="No" selected="true">No</option>
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169 </param>
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170 <when value="Yes">
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171 <param name="extention52" type="integer" value="1" label="in file 2"/>
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172 </when>
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173 <when value="No">
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174 </when>
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175 </conditional>
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176
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177 <conditional name="optionExtentionTroisFile1">
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178 <param name="extentionFile1" type="select" label="Extension towards 3 for file 1">
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179 <option value="Yes">Yes</option>
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180 <option value="No" selected="true">No</option>
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181 </param>
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182 <when value="Yes">
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183 <param name="extention31" type="integer" value="1" label="in file 1" />
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184 </when>
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185 <when value="No">
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186 </when>
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187 </conditional>
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188
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189 <conditional name="optionExtentionTroisFile2">
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190 <param name="extentionFile2" type="select" label="Extension towards 3 for file 2">
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191 <option value="Yes">Yes</option>
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192 <option value="No" selected="true">No</option>
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193 </param>
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194 <when value="Yes">
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195 <param name="extention32" type="integer" value="1" label="in file 2" />
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196 </when>
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197 <when value="No">
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198 </when>
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199 </conditional>
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200
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201 <conditional name="OptionColinearOrAntiSens">
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202 <param name="OptionCA" type="select" label="Colinear or anti-sens">
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203 <option value="Colinear">Colinear</option>
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204 <option value="AntiSens">AntiSens</option>
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205 <option value="NONE" selected="true">NONE</option>
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206 </param>
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207 <when value="Colinear">
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208 </when>
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209 <when value="AntiSens">
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210 </when>
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211 <when value="NONE">
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212 </when>
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213 </conditional>
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214
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215 <conditional name="OptionDistance">
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216 <param name="Dist" type="select" label="Maximum Distance between two reads">
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217 <option value="Yes">Yes</option>
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218 <option value="No" selected="true">No</option>
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219 </param>
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220 <when value="Yes">
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221 <param name="distance" type="integer" value="0"/>
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222 </when>
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223 <when value="No">
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224 </when>
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225 </conditional>
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226
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227 <conditional name="OptionMinOverlap">
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228 <param name="MO" type="select" label="Minimum number of overlapping between two reads">
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229 <option value="Yes">Yes</option>
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230 <option value="No" selected="true">No</option>
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231 </param>
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232 <when value="Yes">
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233 <param name="minOverlap" type="integer" value="1"/>
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234 </when>
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235 <when value="No">
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236 </when>
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237 </conditional>
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238 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
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239 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>
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240 <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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241 <param name="tar" type="boolean" truevalue="--tar" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." />
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242 </inputs>
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243
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244 <outputs>
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245 <data name="outTxtFile" format="txt" label="overlapping output files "/>
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246 <data name="outputTarFile" format="tar">
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247 <filter>tar</filter>
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248 </data>
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249 </outputs>
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250
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251 </tool>
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