18
+ − 1 <tool id="interElementGff" name="interElementGff">
+ − 2 <description>Creates a new Gff output, which corresponds to the region of two successive Elements. </description>
+ − 3 <command interpreter="perl">
+ − 4 interElementGff.pl -i $inputFile
+ − 5
+ − 6 #if $Optionf5ff.option == "Yes":
+ − 7 -f5ff $Optionf5ff.f5ffValue
+ − 8 #end if
+ − 9
+ − 10 #if $Optionff3f.option == "Yes":
+ − 11 -ff3f $Optionff3f.ff3fValue
+ − 12 #end if
+ − 13
+ − 14 #if $Optionf5fr.option == "Yes":
+ − 15 -f5fr $Optionf5fr.f5frValue
+ − 16 #end if
+ − 17
+ − 18 #if $Optionff3r.option == "Yes":
+ − 19 -ff3r $Optionff3r.ff3rValue
+ − 20 #end if
+ − 21
+ − 22 #if $Optionf3rf.option == "Yes":
+ − 23 -f3rf $Optionf3rf.f3rfValue
+ − 24 #end if
+ − 25
+ − 26 #if $Optionfr5f.option == "Yes":
+ − 27 -fr5f $Optionfr5f.fr5fValue
+ − 28 #end if
+ − 29
+ − 30 #if $Optionf3rr.option == "Yes":
+ − 31 -f3rr $Optionf3rr.f3rrValue
+ − 32 #end if
+ − 33
+ − 34 #if $Optionfr5r.option == "Yes":
+ − 35 -fr5r $Optionfr5r.fr5rValue
+ − 36 #end if
+ − 37
+ − 38 #if $Optionr5ff.option == "Yes":
+ − 39 -r5ff $Optionr5ff.r5ffValue
+ − 40 #end if
+ − 41
+ − 42 #if $Optionrf3f.option == "Yes":
+ − 43 -rf3f $Optionrf3f.rf3fValue
+ − 44 #end if
+ − 45
+ − 46 #if $Optionr5fr.option == "Yes":
+ − 47 -r5fr $Optionr5fr.r5frValue
+ − 48 #end if
+ − 49
+ − 50 #if $Optionrf3r.option == "Yes":
+ − 51 -rf3r $Optionrf3r.rf3rValue
+ − 52 #end if
+ − 53
+ − 54 #if $Optionr3rf.option == "Yes":
+ − 55 -r3rf $Optionr3rf.r3rfValue
+ − 56 #end if
+ − 57
+ − 58 #if $Optionrr5f.option == "Yes":
+ − 59 -rr5f $Optionrr5f.rr5fValue
+ − 60 #end if
+ − 61
+ − 62 #if $Optionr3rr.option == "Yes":
+ − 63 -r3rr $Optionr3rr.r3rrValue
+ − 64 #end if
+ − 65
+ − 66 #if $Optionrr5r.option == "Yes":
+ − 67 -rr5r $Optionrr5r.rr5rValue
+ − 68 #end if
+ − 69
+ − 70 -o $outputFile
+ − 71 </command>
+ − 72
+ − 73 <inputs>
+ − 74 <param name="inputFile" type="data" label="Input File" format="gff"/>
+ − 75
+ − 76 <conditional name="Optionf5ff">
+ − 77 <param name="option" type="select" label="Option[f5ff]" help="number of nt to exclude from 5' seed when gene before is Forward, seed is Forward and next gene is Forward [default 0]">
+ − 78 <option value="Yes">Yes</option>
+ − 79 <option value="No" selected="true">No</option>
+ − 80 </param>
+ − 81 <when value="Yes">
+ − 82 <param name="f5ffValue" type="integer" value="10"/>
+ − 83 </when>
+ − 84 <when value="No">
+ − 85 </when>
+ − 86 </conditional>
+ − 87
+ − 88 <conditional name="Optionff3f">
+ − 89 <param name="option" type="select" label="Option[ff3f]">
+ − 90 <option value="Yes">Yes</option>
+ − 91 <option value="No" selected="true">No</option>
+ − 92 </param>
+ − 93 <when value="Yes">
+ − 94 <param name="ff3fValue" type="integer" value="30"/>
+ − 95 </when>
+ − 96 <when value="No">
+ − 97 </when>
+ − 98 </conditional>
+ − 99
+ − 100 <conditional name="Optionf5fr">
+ − 101 <param name="option" type="select" label="Option[f5fr]">
+ − 102 <option value="Yes">Yes</option>
+ − 103 <option value="No" selected="true">No</option>
+ − 104 </param>
+ − 105 <when value="Yes">
+ − 106 <param name="f5frValue" type="integer" value="10"/>
+ − 107 </when>
+ − 108 <when value="No">
+ − 109 </when>
+ − 110 </conditional>
+ − 111
+ − 112 <conditional name="Optionff3r">
+ − 113 <param name="option" type="select" label="Option[ff3r]">
+ − 114 <option value="Yes">Yes</option>
+ − 115 <option value="No" selected="true">No</option>
+ − 116 </param>
+ − 117 <when value="Yes">
+ − 118 <param name="ff3rValue" type="integer" value="-10"/>
+ − 119 </when>
+ − 120 <when value="No">
+ − 121 </when>
+ − 122 </conditional>
+ − 123
+ − 124 <conditional name="Optionf3rf">
+ − 125 <param name="option" type="select" label="Option[f3rf]">
+ − 126 <option value="Yes">Yes</option>
+ − 127 <option value="No" selected="true">No</option>
+ − 128 </param>
+ − 129 <when value="Yes">
+ − 130 <param name="f3rfValue" type="integer" value="-10"/>
+ − 131 </when>
+ − 132 <when value="No">
+ − 133 </when>
+ − 134 </conditional>
+ − 135
+ − 136 <conditional name="Optionfr5f">
+ − 137 <param name="option" type="select" label="Option[fr5f]">
+ − 138 <option value="Yes">Yes</option>
+ − 139 <option value="No" selected="true">No</option>
+ − 140 </param>
+ − 141 <when value="Yes">
+ − 142 <param name="fr5fValue" type="integer" value="10"/>
+ − 143 </when>
+ − 144 <when value="No">
+ − 145 </when>
+ − 146 </conditional>
+ − 147
+ − 148 <conditional name="Optionf3rr">
+ − 149 <param name="option" type="select" label="Option[f3rr]">
+ − 150 <option value="Yes">Yes</option>
+ − 151 <option value="No" selected="true">No</option>
+ − 152 </param>
+ − 153 <when value="Yes">
+ − 154 <param name="f3rrValue" type="integer" value="-10"/>
+ − 155 </when>
+ − 156 <when value="No">
+ − 157 </when>
+ − 158 </conditional>
+ − 159
+ − 160 <conditional name="Optionfr5r">
+ − 161 <param name="option" type="select" label="Option[fr5r]">
+ − 162 <option value="Yes">Yes</option>
+ − 163 <option value="No" selected="true">No</option>
+ − 164 </param>
+ − 165 <when value="Yes">
+ − 166 <param name="fr5rValue" type="integer" value="10"/>
+ − 167 </when>
+ − 168 <when value="No">
+ − 169 </when>
+ − 170 </conditional>
+ − 171
+ − 172 <conditional name="Optionr5ff">
+ − 173 <param name="option" type="select" label="Option[r5ff]">
+ − 174 <option value="Yes">Yes</option>
+ − 175 <option value="No" selected="true">No</option>
+ − 176 </param>
+ − 177 <when value="Yes">
+ − 178 <param name="r5ffValue" type="integer" value="10"/>
+ − 179 </when>
+ − 180 <when value="No">
+ − 181 </when>
+ − 182 </conditional>
+ − 183
+ − 184 <conditional name="Optionrf3f">
+ − 185 <param name="option" type="select" label="Option[rf3f]">
+ − 186 <option value="Yes">Yes</option>
+ − 187 <option value="No" selected="true">No</option>
+ − 188 </param>
+ − 189 <when value="Yes">
+ − 190 <param name="rf3fValue" type="integer" value="30"/>
+ − 191 </when>
+ − 192 <when value="No">
+ − 193 </when>
+ − 194 </conditional>
+ − 195
+ − 196 <conditional name="Optionr5fr">
+ − 197 <param name="option" type="select" label="Option[r5fr]">
+ − 198 <option value="Yes">Yes</option>
+ − 199 <option value="No" selected="true">No</option>
+ − 200 </param>
+ − 201 <when value="Yes">
+ − 202 <param name="r5frValue" type="integer" value="10"/>
+ − 203 </when>
+ − 204 <when value="No">
+ − 205 </when>
+ − 206 </conditional>
+ − 207
+ − 208 <conditional name="Optionrf3r">
+ − 209 <param name="option" type="select" label="Option[rf3r]">
+ − 210 <option value="Yes">Yes</option>
+ − 211 <option value="No" selected="true">No</option>
+ − 212 </param>
+ − 213 <when value="Yes">
+ − 214 <param name="rf3rValue" type="integer" value="-10"/>
+ − 215 </when>
+ − 216 <when value="No">
+ − 217 </when>
+ − 218 </conditional>
+ − 219
+ − 220 <conditional name="Optionr3rf">
+ − 221 <param name="option" type="select" label="Option[r3rf]">
+ − 222 <option value="Yes">Yes</option>
+ − 223 <option value="No" selected="true">No</option>
+ − 224 </param>
+ − 225 <when value="Yes">
+ − 226 <param name="r3rfValue" type="integer" value="30"/>
+ − 227 </when>
+ − 228 <when value="No">
+ − 229 </when>
+ − 230 </conditional>
+ − 231
+ − 232 <conditional name="Optionrr5f">
+ − 233 <param name="option" type="select" label="Option[rr5f]">
+ − 234 <option value="Yes">Yes</option>
+ − 235 <option value="No" selected="true">No</option>
+ − 236 </param>
+ − 237 <when value="Yes">
+ − 238 <param name="rr5fValue" type="integer" value="10"/>
+ − 239 </when>
+ − 240 <when value="No">
+ − 241 </when>
+ − 242 </conditional>
+ − 243
+ − 244 <conditional name="Optionr3rr">
+ − 245 <param name="option" type="select" label="Option[r3rr]">
+ − 246 <option value="Yes">Yes</option>
+ − 247 <option value="No" selected="true">No</option>
+ − 248 </param>
+ − 249 <when value="Yes">
+ − 250 <param name="r3rrValue" type="integer" value="30"/>
+ − 251 </when>
+ − 252 <when value="No">
+ − 253 </when>
+ − 254 </conditional>
+ − 255
+ − 256 <conditional name="Optionrr5r">
+ − 257 <param name="option" type="select" label="Option[rr5r]">
+ − 258 <option value="Yes">Yes</option>
+ − 259 <option value="No" selected="true">No</option>
+ − 260 </param>
+ − 261 <when value="Yes">
+ − 262 <param name="rr5rValue" type="integer" value="10"/>
+ − 263 </when>
+ − 264 <when value="No">
+ − 265 </when>
+ − 266 </conditional>
+ − 267
+ − 268 </inputs>
+ − 269
+ − 270 <outputs>
+ − 271 <data name="outputFile" format="gff" label="[interElementGff] Output File"/>
+ − 272 </outputs>
+ − 273
+ − 274 <help>
+ − 275 command example: interElementGff.pl -i ${i}_annot.gff -o ${i}_trans_IG.gff -f5ff 10 -ff3f 30 -f5fr 10 -ff3r -10 -f3rf -10 -fr5f 10 -f3rr -10 -fr5r 10 -r5ff 10 -rf3f 30 -r5fr 10 -rf3r -10 -r3rf 30 -rr5f 10 -r3rr 30 -rr5r 10
+ − 276 </help>
+ − 277
+ − 278 </tool>
+ − 279
+ − 280
+ − 281
+ − 282
+ − 283
+ − 284
