38
+ − 1 <tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
+ − 2 <description>Extend or shrink a list of genomic coordinates.</description>
+ − 3 <requirements>
+ − 4 <requirement type="set_environment">PYTHONPATH</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
+ − 7 #if $formatType.FormatInputFileName == 'bed':
+ − 8 -f bed
+ − 9 #elif $formatType.FormatInputFileName == 'gff':
+ − 10 -f gff
+ − 11 #elif $formatType.FormatInputFileName == 'gff2':
+ − 12 -f gff2
+ − 13 #elif $formatType.FormatInputFileName == 'gff3':
+ − 14 -f gff3
+ − 15 #elif $formatType.FormatInputFileName == 'sam':
+ − 16 -f sam
+ − 17 #elif $formatType.FormatInputFileName == 'gtf':
+ − 18 -f gtf
+ − 19 #end if
+ − 20
+ − 21 #if $OptionStart.start == "Yes":
+ − 22 -s $OptionStart.startValue
+ − 23 #end if
+ − 24
+ − 25 #if $OptionEnd.end == "Yes":
+ − 26 -e $OptionEnd.endValue
+ − 27 #end if
+ − 28
+ − 29 #if $OptionFivePrim.five == "Yes":
+ − 30 -5 $OptionFivePrim.fivePValue
+ − 31 #end if
+ − 32
+ − 33 #if $OptionTroisP.TroisP == "Yes":
+ − 34 -3 $OptionTroisP.ThreePValue
+ − 35 #end if
+ − 36
+ − 37 -o $outputFile
+ − 38 </command>
+ − 39
+ − 40
+ − 41 <inputs>
+ − 42 <conditional name="formatType">
+ − 43 <param name="FormatInputFileName" type="select" label="Input File Format">
+ − 44 <option value="bed">bed</option>
+ − 45 <option value="gff">gff</option>
+ − 46 <option value="gff2">gff2</option>
+ − 47 <option value="gff3">gff3</option>
+ − 48 <option value="sam">sam</option>
+ − 49 <option value="gtf">gtf</option>
+ − 50 </param>
+ − 51 <when value="bed">
+ − 52 <param name="inputFileName" format="bed" type="data" label="Input File"/>
+ − 53 </when>
+ − 54 <when value="gff">
+ − 55 <param name="inputFileName" format="gff" type="data" label="Input File"/>
+ − 56 </when>
+ − 57 <when value="gff2">
+ − 58 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
+ − 59 </when>
+ − 60 <when value="gff3">
+ − 61 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
+ − 62 </when>
+ − 63 <when value="sam">
+ − 64 <param name="inputFileName" format="sam" type="data" label="Input File"/>
+ − 65 </when>
+ − 66 <when value="gtf">
+ − 67 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
+ − 68 </when>
+ − 69 </conditional>
+ − 70
+ − 71 <conditional name="OptionStart">
+ − 72 <param name="start" type="select" label="shrink to the start of the feature">
+ − 73 <option value="Yes">Yes</option>
+ − 74 <option value="No" selected="true">No</option>
+ − 75 </param>
+ − 76 <when value="Yes">
+ − 77 <param name="startValue" type="integer" value="0"/>
+ − 78 </when>
+ − 79 <when value="No">
+ − 80 </when>
+ − 81 </conditional>
+ − 82
+ − 83 <conditional name="OptionEnd">
+ − 84 <param name="end" type="select" label="shrink to the end of the feature">
+ − 85 <option value="Yes">Yes</option>
+ − 86 <option value="No" selected="true">No</option>
+ − 87 </param>
+ − 88 <when value="Yes">
+ − 89 <param name="endValue" type="integer" value="0"/>
+ − 90 </when>
+ − 91 <when value="No">
+ − 92 </when>
+ − 93 </conditional>
+ − 94
+ − 95
+ − 96 <conditional name="OptionFivePrim">
+ − 97 <param name="five" type="select" label="extend to the 5' direction">
+ − 98 <option value="Yes">Yes</option>
+ − 99 <option value="No" selected="true">No</option>
+ − 100 </param>
+ − 101 <when value="Yes">
+ − 102 <param name="fivePValue" type="integer" value="0"/>
+ − 103 </when>
+ − 104 <when value="No">
+ − 105 </when>
+ − 106 </conditional>
+ − 107
+ − 108 <conditional name="OptionTroisP">
+ − 109 <param name="TroisP" type="select" label="extend to the 3' direction">
+ − 110 <option value="Yes">Yes</option>
+ − 111 <option value="No" selected="true">No</option>
+ − 112 </param>
+ − 113 <when value="Yes">
+ − 114 <param name="ThreePValue" type="integer" value="0"/>
+ − 115 </when>
+ − 116 <when value="No">
+ − 117 </when>
+ − 118 </conditional>
+ − 119
+ − 120
+ − 121 </inputs>
+ − 122
+ − 123 <outputs>
+ − 124 <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/>
+ − 125 </outputs>
+ − 126
+ − 127 <help>
+ − 128 This tool reads a list of transcripts and modifies each feature by:
+ − 129
+ − 130 - shrinking it to the *n* first nucleotides or the *n* last nucleotides, or
+ − 131
+ − 132 - extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
+ − 133
+ − 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!).
+ − 135
+ − 136 The tool needs a transcript file, its format, and outputs a new transcript file.
+ − 137 </help>
+ − 138 </tool>
