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6
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1 <tool id="getDistribution" name="get distribution">
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31
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2 <description>Get Distribution: Get the distribution of the genomic coordinates on a genome.</description>
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6
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3 <command interpreter="python">
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4 ../Java/Python/GetDistribution.py -i $formatType.inputFileName
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5 #if $formatType.FormatInputFileName == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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31
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13 #elif $formatType.FormatInputFileName == 'csv':
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14 -f csv
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6
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15 #elif $formatType.FormatInputFileName == 'sam':
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16 -f sam
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17 #elif $formatType.FormatInputFileName == 'gtf':
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18 -f gtf
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19 #end if
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20
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21 -r $refFile
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22
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23 #if $optionNbBin.Nb == 'Yes':
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24 -b $optionNbBin.nbBins
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25 #end if
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26
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27 #if $optionStart.start == 'Yes':
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28 -s $optionStart.startValue
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29 #end if
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30
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31 #if $optionEnd.end == 'Yes':
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32 -e $optionEnd.endValue
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33 #end if
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34
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35 #if $optionHeight.height == 'Yes':
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36 -H $optionHeight.heightValue
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37 #end if
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38
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39 #if $optionWidth.width == 'Yes':
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40 -W $optionWidth.widthValue
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41 #end if
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42
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43 #if $optionYMin.YMin == 'Yes':
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44 -y $optionYMin.YMinValue
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45 #end if
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46
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47 #if $optionYMax.YMax == 'Yes':
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48 -Y $optionYMax.YMaxValue
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49 #end if
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50
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51 #if $optionChrom.chrom == 'Yes':
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52 -c $optionChrom.chromValue
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53 #end if
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54
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55 #if $optionColor.color == 'Yes':
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56 -l $optionColor.colorValue
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57 #end if
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58
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59 $bothStrands
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60 $average
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61 $normalize
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31
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62 $csv $outputCSV
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63 $gff $outputGFF
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6
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64 -m
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65 -o $outputFile
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66
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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="FormatInputFileName" type="select" label="Input File Format">
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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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31
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76 <option value="csv">csv</option>
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77 <option value="sam">sam</option>
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78 <option value="gtf">gtf</option>
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79 </param>
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80 <when value="bed">
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81 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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82 </when>
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83 <when value="gff">
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84 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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85 </when>
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86 <when value="gff2">
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87 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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88 </when>
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89 <when value="gff3">
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90 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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91 </when>
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31
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92 <when value="csv">
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93 <param name="inputFileName" format="csv" type="data" label="Input File"/>
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94 </when>
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6
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95 <when value="sam">
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96 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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97 </when>
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98 <when value="gtf">
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99 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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100 </when>
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101 </conditional>
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102
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103 <param name="refFile" format="fasta" type="data" label="reference genome file"/>
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104
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105 <conditional name="optionNbBin">
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31
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106 <param name="Nb" type="select" label="number of bins">
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6
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107 <option value="Yes">Yes</option>
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108 <option value="No" selected="true">No</option>
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109 </param>
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110 <when value="Yes">
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111 <param name="nbBins" type="integer" value="1000" />
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112 </when>
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113 <when value="No">
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114 </when>
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115 </conditional>
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116
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117 <conditional name="optionStart">
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31
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118 <param name="start" type="select" label="start from a given region">
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119 <option value="Yes">Yes</option>
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120 <option value="No" selected="true">No</option>
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121 </param>
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122 <when value="Yes">
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123 <param name="startValue" type="integer" value="0" />
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124 </when>
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125 <when value="No">
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126 </when>
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127 </conditional>
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128
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129 <conditional name="optionEnd">
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31
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130 <param name="end" type="select" label="end from a given region">
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131 <option value="Yes">Yes</option>
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132 <option value="No" selected="true">No</option>
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133 </param>
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134 <when value="Yes">
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135 <param name="endValue" type="integer" value="0" />
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136 </when>
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137 <when value="No">
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138 </when>
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139 </conditional>
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140
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141 <conditional name="optionHeight">
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31
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142 <param name="height" type="select" label="height of the graphics">
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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="heightValue" type="integer" value="300" />
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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="optionWidth">
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31
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154 <param name="width" type="select" label="width of the graphics">
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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="widthValue" type="integer" value="1000" />
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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="optionYMin">
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166 <param name="YMin" type="select" label="minimum value on the y-axis to plot">
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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="YMinValue" type="integer" value="1000" />
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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="optionYMax">
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178 <param name="YMax" type="select" label="maximum value on the y-axis to plot">
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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="YMaxValue" type="integer" value="1000" />
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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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31
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189 <conditional name="optionChrom">
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190 <param name="chrom" type="select" label="plot only one given chromosome">
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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="chromValue" type="text" value="chromName" />
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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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6
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201 <conditional name="optionColor">
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202 <param name="color" type="select" label="color of the lines (separated by commas and no space)">
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203 <option value="Yes">Yes</option>
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204 <option value="No" selected="true">No</option>
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205 </param>
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206 <when value="Yes">
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207 <param name="colorValue" type="text" value="red,blue" />
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208 </when>
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209 <when value="No">
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210 </when>
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211 </conditional>
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212
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31
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213
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15
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214 <param name="bothStrands" type="boolean" truevalue="-2" falsevalue="" checked="false" label="plot one curve per strand"/>
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31
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215 <param name="average" type="boolean" truevalue="-a" falsevalue="" checked="false" label="plot plot average (instead of sum)"/>
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6
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216
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15
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217 <conditional name="optionNames">
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218 <param name="names" type="select" label="name for the tags (separated by commas and no space)">
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219 <option value="Yes">Yes</option>
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220 <option value="No" selected="true">No</option>
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221 </param>
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222 <when value="Yes">
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223 <param name="namesValue" type="text" value="nbElements" />
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224 </when>
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225 <when value="No">
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226 </when>
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227 </conditional>
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228
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229 <param name="normalize" type="boolean" truevalue="-z" falsevalue="" checked="false" label="normalize data (when panels are different)"/>
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230 <param name="csv" type="boolean" truevalue="-x" falsevalue="" checked="false" label="write a .csv file."/>
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231 <param name="gff" type="boolean" truevalue="-g" falsevalue="" checked="false" label="write a .gff file."/>
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6
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232 </inputs>
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233
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234 <outputs>
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31
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235 <data name="outputFile" format="png" label="[getDistribution] out png file"/>
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236 <data name="outputCSV" format="csv" label="[getDistribution] output csv file">
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237 <filter>csv</filter>
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238 </data>
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239
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240 <data name="outputGFF" format="gff" label="[getDistribution] output gff file">
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241 <filter>gff</filter>
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242 </data>
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6
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243 </outputs>
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244
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245 <help>
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246 This script gives a .tar out file, if you want to take look at the results, you have to download it.
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6
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247 </help>
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248 </tool>
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