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1 <tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
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2 <description>Extend or shrink a list of genomic coordinates.</description>
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3 <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
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4 #if $formatType.FormatInputFileName == 'bed':
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5 -f bed
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6 #elif $formatType.FormatInputFileName == 'gff':
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7 -f gff
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8 #elif $formatType.FormatInputFileName == 'gff2':
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9 -f gff2
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10 #elif $formatType.FormatInputFileName == 'gff3':
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11 -f gff3
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12 #elif $formatType.FormatInputFileName == 'sam':
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13 -f sam
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14 #elif $formatType.FormatInputFileName == 'gtf':
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15 -f gtf
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16 #end if
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17
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18 #if $OptionStart.start == "Yes":
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19 -s $OptionStart.startValue
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20 #end if
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21
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22 #if $OptionEnd.end == "Yes":
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23 -e $OptionEnd.endValue
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24 #end if
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25
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26 #if $OptionFivePrim.five == "Yes":
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27 -5 $OptionFivePrim.fivePValue
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28 #end if
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29
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30 #if $OptionTroisP.TroisP == "Yes":
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31 -3 $OptionTroisP.ThreePValue
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32 #end if
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33
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34 -o $outputFile
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35 </command>
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36
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37
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38 <inputs>
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39 <conditional name="formatType">
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40 <param name="FormatInputFileName" type="select" label="Input File Format">
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41 <option value="bed">bed</option>
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42 <option value="gff">gff</option>
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43 <option value="gff2">gff2</option>
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44 <option value="gff3">gff3</option>
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45 <option value="sam">sam</option>
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46 <option value="gtf">gtf</option>
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47 </param>
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48 <when value="bed">
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49 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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50 </when>
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51 <when value="gff">
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52 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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53 </when>
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54 <when value="gff2">
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55 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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56 </when>
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57 <when value="gff3">
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58 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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59 </when>
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60 <when value="sam">
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61 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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62 </when>
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63 <when value="gtf">
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64 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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65 </when>
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66 </conditional>
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67
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68 <conditional name="OptionStart">
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69 <param name="start" type="select" label="shrink to the start of the feature">
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70 <option value="Yes">Yes</option>
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71 <option value="No" selected="true">No</option>
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72 </param>
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73 <when value="Yes">
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74 <param name="startValue" type="integer" value="0"/>
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75 </when>
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76 <when value="No">
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77 </when>
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78 </conditional>
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79
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80 <conditional name="OptionEnd">
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81 <param name="end" type="select" label="shrink to the end of the feature">
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82 <option value="Yes">Yes</option>
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83 <option value="No" selected="true">No</option>
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84 </param>
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85 <when value="Yes">
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86 <param name="endValue" type="integer" value="0"/>
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87 </when>
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88 <when value="No">
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89 </when>
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90 </conditional>
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91
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92
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93 <conditional name="OptionFivePrim">
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94 <param name="five" type="select" label="extend to the 5' direction">
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95 <option value="Yes">Yes</option>
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96 <option value="No" selected="true">No</option>
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97 </param>
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98 <when value="Yes">
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99 <param name="fivePValue" type="integer" value="0"/>
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100 </when>
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101 <when value="No">
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102 </when>
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103 </conditional>
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104
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105 <conditional name="OptionTroisP">
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106 <param name="TroisP" type="select" label="extend to the 3' direction">
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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="ThreePValue" type="integer" value="0"/>
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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
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118 </inputs>
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119
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120 <outputs>
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121 <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/>
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122 </outputs>
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123
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124 <help>
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125 This tool reads a list of transcripts and modifies each feature by:
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126
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127 - shrinking it to the *n* first nucleotides or the *n* last nucleotides, or
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128
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129 - extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
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130
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131 Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!).
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132
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133 The tool needs a transcript file, its format, and outputs a new transcript file.
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134 </help>
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135 </tool>
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