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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 <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"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
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7 #if $formatType.FormatInputFileName == 'bed':
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8 -f bed
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9 #elif $formatType.FormatInputFileName == 'gff':
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10 -f gff
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11 #elif $formatType.FormatInputFileName == 'gff2':
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12 -f gff2
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13 #elif $formatType.FormatInputFileName == 'gff3':
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14 -f gff3
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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 #if $OptionStart.start == "Yes":
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22 -s $OptionStart.startValue
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23 #end if
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24
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25 #if $OptionEnd.end == "Yes":
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26 -e $OptionEnd.endValue
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27 #end if
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28
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29 #if $OptionFivePrim.five == "Yes":
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30 -5 $OptionFivePrim.fivePValue
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31 #end if
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32
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33 #if $OptionTroisP.TroisP == "Yes":
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34 -3 $OptionTroisP.ThreePValue
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35 #end if
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36
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37 -o $outputFile
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38 </command>
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39
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40
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41 <inputs>
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42 <conditional name="formatType">
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43 <param name="FormatInputFileName" type="select" label="Input File Format">
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44 <option value="bed">bed</option>
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45 <option value="gff">gff</option>
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46 <option value="gff2">gff2</option>
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47 <option value="gff3">gff3</option>
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48 <option value="sam">sam</option>
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49 <option value="gtf">gtf</option>
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50 </param>
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51 <when value="bed">
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52 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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53 </when>
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54 <when value="gff">
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55 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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56 </when>
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57 <when value="gff2">
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58 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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59 </when>
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60 <when value="gff3">
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61 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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62 </when>
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63 <when value="sam">
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64 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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65 </when>
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66 <when value="gtf">
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67 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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68 </when>
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69 </conditional>
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70
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71 <conditional name="OptionStart">
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72 <param name="start" type="select" label="shrink to the start of the feature">
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73 <option value="Yes">Yes</option>
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74 <option value="No" selected="true">No</option>
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75 </param>
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76 <when value="Yes">
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77 <param name="startValue" type="integer" value="0"/>
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78 </when>
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79 <when value="No">
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80 </when>
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81 </conditional>
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82
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83 <conditional name="OptionEnd">
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84 <param name="end" type="select" label="shrink to the end of the feature">
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85 <option value="Yes">Yes</option>
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86 <option value="No" selected="true">No</option>
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87 </param>
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88 <when value="Yes">
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89 <param name="endValue" type="integer" value="0"/>
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90 </when>
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91 <when value="No">
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92 </when>
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93 </conditional>
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94
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95
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96 <conditional name="OptionFivePrim">
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97 <param name="five" type="select" label="extend to the 5' direction">
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98 <option value="Yes">Yes</option>
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99 <option value="No" selected="true">No</option>
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100 </param>
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101 <when value="Yes">
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102 <param name="fivePValue" type="integer" value="0"/>
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103 </when>
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104 <when value="No">
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105 </when>
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106 </conditional>
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107
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108 <conditional name="OptionTroisP">
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109 <param name="TroisP" type="select" label="extend to the 3' direction">
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110 <option value="Yes">Yes</option>
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111 <option value="No" selected="true">No</option>
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112 </param>
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113 <when value="Yes">
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114 <param name="ThreePValue" type="integer" value="0"/>
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115 </when>
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116 <when value="No">
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117 </when>
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118 </conditional>
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119
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120
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121 </inputs>
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122
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123 <outputs>
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124 <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/>
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125 </outputs>
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126
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127 <help>
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128 This tool reads a list of transcripts and modifies each feature by:
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129
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130 - shrinking it to the *n* first nucleotides or the *n* last nucleotides, or
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131
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132 - extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
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133
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134 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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135
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136 The tool needs a transcript file, its format, and outputs a new transcript file.
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137 </help>
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138 </tool>
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