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1 <tool id="GetDifferentialExpression" name="get differential expression">
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2 <description>Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file.</description>
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3 <command interpreter="python">
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4 ../Java/Python/GetDifferentialExpression.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 -k $formatTypeRef.inputFileNameRef
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35 #if $formatTypeRef.FormatInputFileNameRef == 'bed':
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36 -l bed
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37 #elif $formatTypeRef.FormatInputFileNameRef == 'gff':
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38 -l gff
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39 #elif $formatTypeRef.FormatInputFileNameRef == 'gff2':
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40 -l gff2
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41 #elif $formatTypeRef.FormatInputFileNameRef == 'gff3':
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42 -l gff3
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43 #elif $formatTypeRef.FormatInputFileNameRef == 'sam':
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44 -l sam
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45 #elif $formatTypeRef.FormatInputFileNameRef == 'gtf':
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46 -l gtf
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47 #end if
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48
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49 -o $outputFileGff
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50
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51 $simple
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52 $adjusted
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53
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31
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54
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6
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55 #if $optionSimplePara.simplePara == 'Yes':
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56 -S $optionSimplePara.paraValue
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57 #end if
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58
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59 #if $optionFixedSizeFactor.FSF == 'Yes':
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60 -x $optionFixedSizeFactor.FSFValue
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61 #end if
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62
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63 #if $optionFDR.FDR == 'Yes':
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64 -d $optionFDR.FDRValue
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65 #end if
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31
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66 $plot $outputFilePNG
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67 </command>
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68
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69 <inputs>
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70 <conditional name="formatType">
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71 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
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72 <option value="bed">bed</option>
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73 <option value="gff">gff</option>
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74 <option value="gff2">gff2</option>
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75 <option value="gff3">gff3</option>
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76 <option value="sam">sam</option>
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77 <option value="gtf">gtf</option>
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78 </param>
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79 <when value="bed">
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80 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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81 </when>
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82 <when value="gff">
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83 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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84 </when>
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85 <when value="gff2">
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86 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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87 </when>
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88 <when value="gff3">
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89 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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90 </when>
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91 <when value="sam">
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92 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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93 </when>
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94 <when value="gtf">
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95 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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96 </when>
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97 </conditional>
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98
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99 <conditional name="formatType2">
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100 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
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101 <option value="bed">bed</option>
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102 <option value="gff">gff</option>
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103 <option value="gff2">gff2</option>
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104 <option value="gff3">gff3</option>
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105 <option value="sam">sam</option>
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106 <option value="gtf">gtf</option>
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107 </param>
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108 <when value="bed">
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109 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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110 </when>
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111 <when value="gff">
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112 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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113 </when>
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114 <when value="gff2">
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115 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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116 </when>
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117 <when value="gff3">
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118 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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119 </when>
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120 <when value="sam">
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121 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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122 </when>
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123 <when value="gtf">
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124 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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125 </when>
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126 </conditional>
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127
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128 <conditional name="formatTypeRef">
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129 <param name="FormatInputFileNameRef" type="select" label="Input Ref File Format ">
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130 <option value="bed">bed</option>
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131 <option value="gff">gff</option>
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132 <option value="gff2">gff2</option>
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133 <option value="gff3">gff3</option>
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134 <option value="sam">sam</option>
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135 <option value="gtf">gtf</option>
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136 </param>
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137 <when value="bed">
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138 <param name="inputFileNameRef" format="bed" type="data" label="Input Ref File"/>
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139 </when>
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140 <when value="gff">
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141 <param name="inputFileNameRef" format="gff" type="data" label="Input Ref File"/>
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142 </when>
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143 <when value="gff2">
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144 <param name="inputFileNameRef" format="gff2" type="data" label="Input Ref File"/>
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145 </when>
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146 <when value="gff3">
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147 <param name="inputFileNameRef" format="gff3" type="data" label="Input Ref File"/>
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148 </when>
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149 <when value="sam">
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150 <param name="inputFileNameRef" format="sam" type="data" label="Input Ref File"/>
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151 </when>
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152 <when value="gtf">
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153 <param name="inputFileNameRef" format="gtf" type="data" label="Input Ref File"/>
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154 </when>
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155 </conditional>
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156
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157 <param name="simple" type="boolean" truevalue="-s" falsevalue="" checked="false" label="normalize using the number of reads in each condition"/>
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158 <param name="adjusted" type="boolean" truevalue="-a" falsevalue="" checked="false" label="normalize using the number of reads of 'mean' regions"/>
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159
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160 <conditional name="optionSimplePara">
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161 <param name="simplePara" type="select" label="provide the number of reads" >
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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="paraValue" type="text" value="None" label="provide the number of reads" />
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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="optionFixedSizeFactor">
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173 <param name="FSF" type="select" label="give the magnification factor for the normalization using fixed size sliding windows in reference regions (leave empty for no such normalization)">
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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="FSFValue" type="integer" value="0" />
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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="optionFDR">
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185 <param name="FDR" type="select" label="use FDR">
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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="FDRValue" type="float" value="0.0"/>
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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 <param name="plot" type="boolean" truevalue="-p" falsevalue="" checked="false" label="plot option" help="plot cloud plot"/>
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197
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198 </inputs>
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199
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200 <outputs>
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201 <data name="outputFileGff" format="gff3" label="[GetDifferentialExpression]out file"/>
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202 <data name="outputFilePNG" format="PNG" label="[GetDifferentialExpression]PNG file">
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203 <filter>plot</filter>
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204 </data>
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205 </outputs>
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206
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207 <help>
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208 example: python GetDifferentialExpression.py -i input1 -f gff3 -j input2 -g gff3 -k ref -l gff3 -o output.gff3
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209 </help>
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210 </tool>
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