6
+ − 1 <tool id="CompareOverlapping" name="Compare Overlapping">
+ − 2 <description>Print all the transcripts from a first file which overlap with the transcripts from a second file.</description>
+ − 3 <command interpreter="python">
+ − 4 ../Java/Python/CompareOverlapping.py -i $formatType.inputFileName1
+ − 5 #if $formatType.FormatInputFileName1 == 'bed':
+ − 6 -f bed
+ − 7 #elif $formatType.FormatInputFileName1 == 'gff':
+ − 8 -f gff
+ − 9 #elif $formatType.FormatInputFileName1 == 'gff2':
+ − 10 -f gff2
+ − 11 #elif $formatType.FormatInputFileName1 == 'gff3':
+ − 12 -f gff3
+ − 13 #elif $formatType.FormatInputFileName1 == 'sam':
+ − 14 -f sam
+ − 15 #elif $formatType.FormatInputFileName1 == 'gtf':
+ − 16 -f gtf
+ − 17 #end if
+ − 18
+ − 19 -j $formatType2.inputFileName2
+ − 20 #if $formatType2.FormatInputFileName2 == 'bed':
+ − 21 -g bed
+ − 22 #elif $formatType2.FormatInputFileName2 == 'gff':
+ − 23 -g gff
+ − 24 #elif $formatType2.FormatInputFileName2 == 'gff2':
+ − 25 -g gff2
+ − 26 #elif $formatType2.FormatInputFileName2 == 'gff3':
+ − 27 -g gff3
+ − 28 #elif $formatType2.FormatInputFileName2 == 'sam':
+ − 29 -g sam
+ − 30 #elif $formatType2.FormatInputFileName2 == 'gtf':
+ − 31 -g gtf
+ − 32 #end if
+ − 33
+ − 34 -o $outputFileGff
+ − 35
+ − 36 #if $optionNFirstFile1.NFirstForFile1 == 'Yes':
+ − 37 -S $optionNFirstFile1.firstNtFile1
+ − 38 #end if
+ − 39 #if $optionNFirstFile2.NFirstForFile2 == 'Yes':
+ − 40 -s $optionNFirstFile2.firstNtFile2
+ − 41 #end if
+ − 42 #if $optionNLastFile1.NLastForFile1 == 'Yes':
+ − 43 -U $optionNLastFile1.lastNtFile1
+ − 44 #end if
+ − 45 #if $optionNLastFile2.NLastForFile2 == 'Yes':
+ − 46 -u $optionNLastFile2.lastNtFile2
+ − 47 #end if
+ − 48
+ − 49 #if $optionExtentionCinqFile1.extentionFile1 == 'Yes':
+ − 50 -E $optionExtentionCinqFile1.extention51
+ − 51 #end if
+ − 52 #if $optionExtentionCinqFile2.extentionFile2 == 'Yes':
+ − 53 -e $optionExtentionCinqFile2.extention52
+ − 54 #end if
+ − 55
+ − 56 #if $optionExtentionTroisFile1.extentionFile1 == 'Yes':
+ − 57 -N $optionExtentionTroisFile1.extention31
+ − 58 #end if
+ − 59 #if $optionExtentionTroisFile2.extentionFile2 == 'Yes':
+ − 60 -n $optionExtentionTroisFile2.extention32
+ − 61 #end if
+ − 62
+ − 63 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
+ − 64 -c
+ − 65 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
+ − 66 -a
+ − 67 #end if
+ − 68
+ − 69 #if $OptionDistance.Dist == 'Yes':
+ − 70 -d $OptionDistance.distance
+ − 71 #end if
+ − 72
+ − 73 #if $OptionMinOverlap.MO == 'Yes':
+ − 74 -m $OptionMinOverlap.minOverlap
+ − 75 #end if
+ − 76
+ − 77 $InvertMatch
+ − 78 $ReportIntron
+ − 79 $NotOverlapping
+ − 80
+ − 81 </command>
+ − 82
+ − 83 <inputs>
+ − 84 <conditional name="formatType">
+ − 85 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
+ − 86 <option value="bed">bed</option>
+ − 87 <option value="gff">gff</option>
+ − 88 <option value="gff2">gff2</option>
+ − 89 <option value="gff3">gff3</option>
+ − 90 <option value="sam">sam</option>
+ − 91 <option value="gtf">gtf</option>
+ − 92 </param>
+ − 93 <when value="bed">
+ − 94 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
+ − 95 </when>
+ − 96 <when value="gff">
+ − 97 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
+ − 98 </when>
+ − 99 <when value="gff2">
+ − 100 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
+ − 101 </when>
+ − 102 <when value="gff3">
+ − 103 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
+ − 104 </when>
+ − 105 <when value="sam">
+ − 106 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
+ − 107 </when>
+ − 108 <when value="gtf">
+ − 109 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
+ − 110 </when>
+ − 111 </conditional>
+ − 112
+ − 113 <conditional name="formatType2">
+ − 114 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
+ − 115 <option value="bed">bed</option>
+ − 116 <option value="gff">gff</option>
+ − 117 <option value="gff2">gff2</option>
+ − 118 <option value="gff3">gff3</option>
+ − 119 <option value="sam">sam</option>
+ − 120 <option value="gtf">gtf</option>
+ − 121 </param>
+ − 122 <when value="bed">
+ − 123 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
+ − 124 </when>
+ − 125 <when value="gff">
+ − 126 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
+ − 127 </when>
+ − 128 <when value="gff2">
+ − 129 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
+ − 130 </when>
+ − 131 <when value="gff3">
+ − 132 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
+ − 133 </when>
+ − 134 <when value="sam">
+ − 135 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
+ − 136 </when>
+ − 137 <when value="gtf">
+ − 138 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
+ − 139 </when>
+ − 140 </conditional>
+ − 141
+ − 142
+ − 143
+ − 144 <conditional name="optionNFirstFile1">
+ − 145 <param name="NFirstForFile1" type="select" label="NFirst for file 1" help="only consider the n first nucleotides of the transcripts in file 1">
+ − 146 <option value="Yes">Yes</option>
+ − 147 <option value="No" selected="true">No</option>
+ − 148 </param>
+ − 149 <when value="Yes">
+ − 150 <param name="firstNtFile1" type="integer" value="1" label="n first nucleotides for input file 1" />
+ − 151 </when>
+ − 152 <when value="No">
+ − 153 </when>
+ − 154 </conditional>
+ − 155 <conditional name="optionNFirstFile2">
+ − 156 <param name="NFirstForFile2" type="select" label="NFirst for file 2" help="only consider the n first nucleotides of the transcripts in file 2">
+ − 157 <option value="Yes">Yes</option>
+ − 158 <option value="No" selected="true">No</option>
+ − 159 </param>
+ − 160 <when value="Yes">
+ − 161 <param name="firstNtFile2" type="integer" value="1" label="n first nucleotides for input file 1" />
+ − 162 </when>
+ − 163 <when value="No">
+ − 164 </when>
+ − 165 </conditional>
+ − 166
+ − 167 <conditional name="optionNLastFile1">
+ − 168 <param name="NLastForFile1" type="select" label="NLast for file 1">
+ − 169 <option value="Yes">Yes</option>
+ − 170 <option value="No" selected="true">No</option>
+ − 171 </param>
+ − 172 <when value="Yes">
+ − 173 <param name="lastNtFile1" type="integer" value="1" label="n last nucleotides for input file 1" help="only consider the n last nucleotides of the transcripts in file 1"/>
+ − 174 </when>
+ − 175 <when value="No">
+ − 176 </when>
+ − 177 </conditional>
+ − 178 <conditional name="optionNLastFile2">
+ − 179 <param name="NLastForFile2" type="select" label="NLast for file 2">
+ − 180 <option value="Yes">Yes</option>
+ − 181 <option value="No" selected="true">No</option>
+ − 182 </param>
+ − 183 <when value="Yes">
+ − 184 <param name="lastNtFile2" type="integer" value="1" label="n last nucleotides for input file 2" help="only consider the n last nucleotides of the transcripts in file 2"/>
+ − 185 </when>
+ − 186 <when value="No">
+ − 187 </when>
+ − 188 </conditional>
+ − 189
+ − 190
+ − 191
+ − 192 <conditional name="optionExtentionCinqFile1">
+ − 193 <param name="extentionFile1" type="select" label="Extension towards 5 for file 1">
+ − 194 <option value="Yes">Yes</option>
+ − 195 <option value="No" selected="true">No</option>
+ − 196 </param>
+ − 197 <when value="Yes">
+ − 198 <param name="extention51" type="integer" value="1" label="in file 1" />
+ − 199 </when>
+ − 200 <when value="No">
+ − 201 </when>
+ − 202 </conditional>
+ − 203
+ − 204
+ − 205 <conditional name="optionExtentionCinqFile2">
+ − 206 <param name="extentionFile2" type="select" label="Extension towards 5 for file 2">
+ − 207 <option value="Yes">Yes</option>
+ − 208 <option value="No" selected="true">No</option>
+ − 209 </param>
+ − 210 <when value="Yes">
+ − 211 <param name="extention52" type="integer" value="1" label="in file 2"/>
+ − 212 </when>
+ − 213 <when value="No">
+ − 214 </when>
+ − 215 </conditional>
+ − 216
+ − 217 <conditional name="optionExtentionTroisFile1">
+ − 218 <param name="extentionFile1" type="select" label="Extension towards 3 for file 1">
+ − 219 <option value="Yes">Yes</option>
+ − 220 <option value="No" selected="true">No</option>
+ − 221 </param>
+ − 222 <when value="Yes">
+ − 223 <param name="extention31" type="integer" value="1" label="in file 1" />
+ − 224 </when>
+ − 225 <when value="No">
+ − 226 </when>
+ − 227 </conditional>
+ − 228
+ − 229 <conditional name="optionExtentionTroisFile2">
+ − 230 <param name="extentionFile2" type="select" label="Extension towards 3 for file 2">
+ − 231 <option value="Yes">Yes</option>
+ − 232 <option value="No" selected="true">No</option>
+ − 233 </param>
+ − 234 <when value="Yes">
+ − 235 <param name="extention32" type="integer" value="1" label="in file 2" />
+ − 236 </when>
+ − 237 <when value="No">
+ − 238 </when>
+ − 239 </conditional>
+ − 240
+ − 241 <conditional name="OptionColinearOrAntiSens">
+ − 242 <param name="OptionCA" type="select" label="Colinear or anti-sens">
+ − 243 <option value="Colinear">Colinear</option>
+ − 244 <option value="AntiSens">AntiSens</option>
+ − 245 <option value="NONE" selected="true">NONE</option>
+ − 246 </param>
+ − 247 <when value="Colinear">
+ − 248 </when>
+ − 249 <when value="AntiSens">
+ − 250 </when>
+ − 251 <when value="NONE">
+ − 252 </when>
+ − 253 </conditional>
+ − 254
+ − 255 <conditional name="OptionDistance">
+ − 256 <param name="Dist" type="select" label="Maximum Distance between two reads">
+ − 257 <option value="Yes">Yes</option>
+ − 258 <option value="No" selected="true">No</option>
+ − 259 </param>
+ − 260 <when value="Yes">
+ − 261 <param name="distance" type="integer" value="0"/>
+ − 262 </when>
+ − 263 <when value="No">
+ − 264 </when>
+ − 265 </conditional>
+ − 266
+ − 267 <conditional name="OptionMinOverlap">
+ − 268 <param name="MO" type="select" label="Minimum number of overlapping between two reads">
+ − 269 <option value="Yes">Yes</option>
+ − 270 <option value="No" selected="true">No</option>
+ − 271 </param>
+ − 272 <when value="Yes">
+ − 273 <param name="minOverlap" type="integer" value="1"/>
+ − 274 </when>
+ − 275 <when value="No">
+ − 276 </when>
+ − 277 </conditional>
+ − 278 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
+ − 279 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Report intron"/>
+ − 280 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
+ − 281
+ − 282 </inputs>
+ − 283
+ − 284 <outputs>
+ − 285 <data name="outputFileGff" format="gff3"/>
+ − 286 </outputs>
+ − 287
+ − 288 </tool>
