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1 <tool id="plotCoverage" name="plot coverage">
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2 <description>Plot the coverage of the first data with respect to the second one.</description>
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3 <command interpreter="python">
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4 ../Java/Python/WrappPlotCoverage.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
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35 #if $optionRef.Ref == 'Yes':
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36 -q $optionRef.inputSequenceFile
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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.widthVal
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41 #end if
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42 #if $optionheight.height == 'Yes':
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43 -e $optionheight.heightVal
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44 #end if
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45 #if $optionXlab.Xlab == 'Yes':
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46 -x $optionXlab.XlabVal
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47 #end if
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48 #if $optionYlab.Ylab == 'Yes':
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49 -y $optionYlab.YlabVal
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50 #end if
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51 #if $optiontitle.title == 'Yes':
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52 -t $optiontitle.titleVal
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53 #end if
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54
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55 #if $optionplusColor.plusColor == 'Yes':
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56 -p $optionplusColor.plusColorVal
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57 #end if
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58 #if $optionminusColor.minusColor == 'Yes':
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59 -m $optionminusColor.minusColorVal
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60 #end if
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61
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62 #if $optionsumColor.sumColor == 'Yes':
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63 -s $optionsumColor.sumColorVal
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64 #end if
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65 #if $optionlineColor.lineColor == 'Yes':
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66 -l $optionlineColor.lineColorVal
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67 #end if
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68
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69 $merge
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70 -o $outputFile
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71 </command>
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72
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73 <inputs>
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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 <conditional name="formatType2">
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104 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
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105 <option value="bed">bed</option>
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106 <option value="gff">gff</option>
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107 <option value="gff2">gff2</option>
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108 <option value="gff3">gff3</option>
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109 <option value="gff2">sam</option>
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110 <option value="gff3">gtf</option>
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111 </param>
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112 <when value="bed">
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113 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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114 </when>
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115 <when value="gff">
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116 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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117 </when>
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118 <when value="gff2">
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119 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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120 </when>
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121 <when value="gff3">
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122 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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123 </when>
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124 <when value="sam">
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125 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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126 </when>
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127 <when value="gtf">
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128 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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129 </when>
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130 </conditional>
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131
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132 <conditional name="optionRef">
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133 <param name="Ref" type="select" label="reference sequence file">
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134 <option value="Yes">Yes</option>
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135 <option value="No" selected="true">No</option>
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136 </param>
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137 <when value="Yes">
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138 <param name="inputSequenceFile" format="fasta" type="data" value="None"/>
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139 </when>
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140 <when value="No">
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141 </when>
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142 </conditional>
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143
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144
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145
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146
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147 <conditional name="optionwidth">
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148 <param name="width" type="select" label="width of the plots (in px)">
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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="widthVal" type="integer" value="1500" />
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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="optionheight">
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160 <param name="height" type="select" label="height of the plots (in px)">
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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="heightVal" type="integer" value="1000" />
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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 <conditional name="optiontitle">
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172 <param name="title" type="select" label="title of the plots ">
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173 <option value="Yes">Yes</option>
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174 <option value="No" selected="true">No</option>
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175 </param>
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176 <when value="Yes">
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177 <param name="titleVal" type="text" value=" " />
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178 </when>
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179 <when value="No">
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180 </when>
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181 </conditional>
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182
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183 <conditional name="optionXlab">
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184 <param name="Xlab" type="select" label="label on the x-axis">
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185 <option value="Yes">Yes</option>
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186 <option value="No" selected="true">No</option>
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187 </param>
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188 <when value="Yes">
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189 <param name="XlabVal" type="text" value=" "/>
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190 </when>
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191 <when value="No">
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192 </when>
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193 </conditional>
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194
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195 <conditional name="optionYlab">
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196 <param name="Ylab" type="select" label="label on the y-axis">
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197 <option value="Yes">Yes</option>
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198 <option value="No" selected="true">No</option>
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199 </param>
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200 <when value="Yes">
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201 <param name="YlabVal" type="text" value=" " />
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202 </when>
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203 <when value="No">
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204 </when>
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205 </conditional>
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206
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207 <conditional name="optionplusColor">
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208 <param name="plusColor" type="select" label="color for the elements on the plus strand">
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209 <option value="Yes">Yes</option>
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210 <option value="No" selected="true">No</option>
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211 </param>
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212 <when value="Yes">
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213 <param name="plusColorVal" type="text" value="red"/>
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214 </when>
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215 <when value="No">
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216 </when>
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217 </conditional>
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218
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219 <conditional name="optionminusColor">
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220 <param name="minusColor" type="select" label="color for the elements on the minus strand">
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221 <option value="Yes">Yes</option>
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222 <option value="No" selected="true">No</option>
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223 </param>
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224 <when value="Yes">
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225 <param name="minusColorVal" type="text" value="blue"/>
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226 </when>
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227 <when value="No">
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228 </when>
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229 </conditional>
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230
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231 <conditional name="optionsumColor">
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232 <param name="sumColor" type="select" label="color for 2 strands coverage line">
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233 <option value="Yes">Yes</option>
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234 <option value="No" selected="true">No</option>
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235 </param>
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236 <when value="Yes">
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237 <param name="sumColorVal" type="text" value="black"/>
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238 </when>
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239 <when value="No">
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240 </when>
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241 </conditional>
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242
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243 <conditional name="optionlineColor">
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244 <param name="lineColor" type="select" label="color for the lines">
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245 <option value="Yes">Yes</option>
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246 <option value="No" selected="true">No</option>
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247 </param>
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248 <when value="Yes">
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249 <param name="lineColorVal" type="text" value="black"/>
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250 </when>
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251 <when value="No">
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252 </when>
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253 </conditional>
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254
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255 <param name="merge" type="boolean" truevalue="-1" falsevalue="" checked="false" label="merge the 2 plots in 1"/>
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256 </inputs>
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257
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258 <outputs>
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259 <data name="outputFile" format="tar" label="[plotCoverage] tar out file" help="You can not see the results directly from galaxy, but you can download this tar output file."/>
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260 </outputs>
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261
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262 <help>
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263 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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264 </help>
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265 </tool>
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