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1 <tool id="mergeTranscriptLists" name="merge transcript lists">
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2 <description>Merge the elements of two lists of genomic coordinates.</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1
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8 #if $formatType.FormatInputFileName1 == 'bed':
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9 -f bed
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10 #elif $formatType.FormatInputFileName1 == 'gff':
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11 -f gff
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12 #elif $formatType.FormatInputFileName1 == 'gff2':
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13 -f gff2
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14 #elif $formatType.FormatInputFileName1 == 'gff3':
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15 -f gff3
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16 #elif $formatType.FormatInputFileName1 == 'sam':
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17 -f sam
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18 #elif $formatType.FormatInputFileName1 == 'gtf':
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19 -f gtf
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20 #end if
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21
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22 -j $formatType2.inputFileName2
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23 #if $formatType2.FormatInputFileName2 == 'bed':
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24 -g bed
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25 #elif $formatType2.FormatInputFileName2 == 'gff':
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26 -g gff
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27 #elif $formatType2.FormatInputFileName2 == 'gff2':
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28 -g gff2
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29 #elif $formatType2.FormatInputFileName2 == 'gff3':
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30 -g gff3
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31 #elif $formatType2.FormatInputFileName2 == 'sam':
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32 -g sam
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33 #elif $formatType2.FormatInputFileName2 == 'gtf':
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34 -g gtf
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35 #end if
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36
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37 $all
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38 $normalize
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39
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40 #if $OptionDistance.dis == 'Yes':
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41 -d $OptionDistance.disVal
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42 #end if
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43
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44 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
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45 -c
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46 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
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47 -a
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48 #end if
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49
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50 -o $outputFileGff
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51 </command>
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52
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53 <inputs>
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54 <conditional name="formatType">
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55 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
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56 <option value="bed">bed</option>
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57 <option value="gff">gff</option>
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58 <option value="gff2">gff2</option>
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59 <option value="gff3">gff3</option>
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60 <option value="sam">sam</option>
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61 <option value="gtf">gtf</option>
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62 </param>
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63 <when value="bed">
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64 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
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65 </when>
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66 <when value="gff">
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67 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
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68 </when>
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69 <when value="gff2">
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70 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
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71 </when>
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72 <when value="gff3">
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73 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
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74 </when>
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75 <when value="sam">
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76 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
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77 </when>
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78 <when value="gtf">
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79 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
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80 </when>
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81 </conditional>
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82
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83 <conditional name="formatType2">
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84 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
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85 <option value="bed">bed</option>
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86 <option value="gff">gff</option>
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87 <option value="gff2">gff2</option>
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88 <option value="gff3">gff3</option>
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89 <option value="sam">sam</option>
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90 <option value="gtf">gtf</option>
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91 </param>
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92 <when value="bed">
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93 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
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94 </when>
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95 <when value="gff">
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96 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
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97 </when>
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98 <when value="gff2">
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99 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
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100 </when>
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101 <when value="gff3">
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102 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
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103 </when>
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104 <when value="sam">
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105 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
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106 </when>
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107 <when value="gtf">
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108 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
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109 </when>
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110 </conditional>
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111
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112
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113 <param name="all" type="boolean" truevalue="-k" falsevalue="" checked="false" label="print all the transcripts, not only those overlapping"/>
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114 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize the number of reads per cluster by the number of mappings per read "/>
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115
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116 <conditional name="OptionDistance">
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117 <param name="dis" type="select" label="provide the number of reads" >
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118 <option value="Yes">Yes</option>
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119 <option value="No" selected="true">No</option>
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120 </param>
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121 <when value="Yes">
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122 <param name="disVal" type="integer" value="0" label="max. distance between two transcripts" />
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123 </when>
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124 <when value="No">
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125 </when>
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126 </conditional>
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127
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128 <conditional name="OptionColinearOrAntiSens">
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129 <param name="OptionCA" type="select" label="Colinear or anti-sens">
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130 <option value="Colinear">Colinear</option>
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131 <option value="AntiSens">AntiSens</option>
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132 <option value="NONE" selected="true">NONE</option>
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133 </param>
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134 <when value="Colinear">
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135 </when>
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136 <when value="AntiSens">
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137 </when>
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138 <when value="NONE">
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139 </when>
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140 </conditional>
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141
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142 </inputs>
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143
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144 <outputs>
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145 <data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/>
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146 </outputs>
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147
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148 <help>
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149 The script is similar to *compare overlapping*, except that when data of two different sets overlap, they are merged. You can use the same parameters as *compare overlapping* and use them to look for transcription on both strands, for example.
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150
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151 Optionally, you can also add to the output all the elements from the first set which do not overlap with the second set.
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152 </help>
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153 </tool>
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