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1 <tool id="GetFlanking" name="get flanking">
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2 <description>Get the flanking regions of a set of reference.</description>
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3 <command interpreter="python">
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4 ../Java/Python/GetFlanking.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 -j $formatType2.inputFileName2
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20 #if $formatType2.FormatInputFileName2 == 'bed':
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21 -g bed
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22 #elif $formatType2.FormatInputFileName2 == 'gff':
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23 -g gff
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24 #elif $formatType2.FormatInputFileName2 == 'gff2':
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25 -g gff2
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26 #elif $formatType2.FormatInputFileName2 == 'gff3':
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27 -g gff3
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28 #elif $formatType2.FormatInputFileName2 == 'sam':
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29 -g sam
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30 #elif $formatType2.FormatInputFileName2 == 'gtf':
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31 -g gtf
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32 #end if
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33
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34 #if $OptionUpDownStream.OptionUD == 'UpStream':
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35 -5
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36 #elif $OptionUpDownStream.OptionUD == 'DownStream':
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37 -3
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38 #end if
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39
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40
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41 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
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42 -c
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43 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
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44 -a
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45 #end if
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46
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47 #if $OptionMax.maximum == "Yes":
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48 -D $OptionMax.max
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49 #end if
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50 #if $OptionMin.minimum == "Yes":
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51 -d $OptionMin.min
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52 #end if
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53
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54 -o $outputFile
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55
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56
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57
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58 </command>
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59
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60 <inputs>
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61 <conditional name="formatType">
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62 <param name="FormatInputFileName1" type="select" label="query File Format">
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63 <option value="bed">bed</option>
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64 <option value="gff">gff</option>
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65 <option value="gff2">gff2</option>
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66 <option value="gff3">gff3</option>
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67 <option value="sam">sam</option>
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68 <option value="gtf">gtf</option>
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69 </param>
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70 <when value="bed">
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71 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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72 </when>
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73 <when value="gff">
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74 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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75 </when>
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76 <when value="gff2">
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77 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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78 </when>
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79 <when value="gff3">
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80 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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81 </when>
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82 <when value="sam">
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83 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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84 </when>
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85 <when value="gtf">
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86 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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87 </when>
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88 </conditional>
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89
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90 <conditional name="formatType2">
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91 <param name="FormatInputFileName2" type="select" label="Refence File Format">
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92 <option value="bed">bed</option>
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93 <option value="gff">gff</option>
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94 <option value="gff2">gff2</option>
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95 <option value="gff3">gff3</option>
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96 <option value="sam">sam</option>
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97 <option value="gtf">gtf</option>
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98 </param>
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99 <when value="bed">
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100 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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101 </when>
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102 <when value="gff">
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103 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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104 </when>
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105 <when value="gff2">
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106 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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107 </when>
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108 <when value="gff3">
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109 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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110 </when>
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111 <when value="sam">
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112 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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113 </when>
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114 <when value="gtf">
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115 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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116 </when>
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117 </conditional>
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118
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119 <conditional name="OptionUpDownStream">
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120 <param name="OptionUD" type="select" label="UpStream or DownStream">
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121 <option value="UpStream">UpStream</option>
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122 <option value="DownStream">DownStream</option>
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123 <option value="NONE" selected="true">NONE</option>
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124 </param>
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125 <when value="UpStream">
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126 </when>
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127 <when value="DownStream">
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128 </when>
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129 <when value="NONE">
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130 </when>
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131 </conditional>
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132
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133 <conditional name="OptionColinearOrAntiSens">
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134 <param name="OptionCA" type="select" label="Colinear or anti-sens">
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135 <option value="Colinear">Colinear</option>
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136 <option value="AntiSens">AntiSens</option>
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137 <option value="NONE" selected="true">NONE</option>
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138 </param>
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139 <when value="Colinear">
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140 </when>
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141 <when value="AntiSens">
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142 </when>
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143 <when value="NONE">
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144 </when>
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145 </conditional>
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146
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147 <conditional name="OptionMax">
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148 <param name="maximum" type="select" label="maximum distance between 2 elements">
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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="max" 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
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159 <conditional name="OptionMin">
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160 <param name="minimum" type="select" label="minimum distance between 2 elements">
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161 <option value="Yes">Yes</option>
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162 <option value="No" selected="true">No</option>
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163 </param>
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164 <when value="Yes">
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165 <param name="min" type="integer" value="0" />
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166 </when>
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167 <when value="No">
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168 </when>
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169 </conditional>
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170
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171 </inputs>
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172
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173
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174 <outputs>
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175 <data format="gff3" name="outputFile" label="[GetFlanking] Output File"/>
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176 </outputs>
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177
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178
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179 </tool>
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