6
+ − 1 <tool id="GetDistance" name="get distance">
+ − 2 <description>Give the distances between every data from the first input set and the data from the second input set</description>
+ − 3 <command interpreter="python">
+ − 4 ../Java/Python/getDistance.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
+ − 35 $absolute $proportion
+ − 36
+ − 37 #if $OptionColinearOrAntiSens.OptionCA == "Colinear":
+ − 38 -c
+ − 39 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
+ − 40 -a
+ − 41 #end if
+ − 42
+ − 43 #if $OptionFirstNucl5.FirstNu5 == "Yes":
+ − 44 -s $OptionFirstNucl5.first5File1
+ − 45 -S $OptionFirstNucl5.first5File2
+ − 46 #end if
+ − 47
+ − 48 #if $OptionFirstNucl3.FirstNu3 == "Yes":
+ − 49 -e $OptionFirstNucl3.first3File1
+ − 50 -E $OptionFirstNucl3.first3File2
+ − 51 #end if
+ − 52
+ − 53 #if $OptionMinDistance.MinD == "Yes":
+ − 54 -m $OptionMinDistance.minDistance
+ − 55 #end if
+ − 56
+ − 57 #if $OptionMaxDistance.MaxD == "Yes":
+ − 58 -M $OptionMaxDistance.maxDistance
+ − 59 #end if
+ − 60
+ − 61 $fivePrime $threePrime $spearMan
+ − 62
+ − 63 #if $OptionBuckets.OBuckets == "Yes":
+ − 64 -u $OptionBuckets.buckets
+ − 65 #end if
+ − 66
+ − 67 #if $OptionMinXaxis.MinX == "Yes":
+ − 68 -x $OptionMinXaxis.minXaxis
+ − 69 #end if
+ − 70
+ − 71 #if $OptionMaxXaxis.MaxX == "Yes":
+ − 72 -X $OptionMaxXaxis.maxXaxis
+ − 73 #end if
+ − 74
+ − 75 #if $OptionTitle.OTitle == "Yes":
+ − 76 -t $OptionTitle.title
+ − 77 #end if
+ − 78
+ − 79 -o $outputFilePng
+ − 80 $outputDistance $outputFileDistance
+ − 81
+ − 82 </command>
+ − 83
+ − 84 <inputs>
+ − 85 <conditional name="formatType">
+ − 86 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
+ − 87 <option value="bed">bed</option>
+ − 88 <option value="gff">gff</option>
+ − 89 <option value="gff2">gff2</option>
+ − 90 <option value="gff3">gff3</option>
+ − 91 <option value="sam">sam</option>
+ − 92 <option value="gtf">gtf</option>
+ − 93 </param>
+ − 94 <when value="bed">
+ − 95 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
+ − 96 </when>
+ − 97 <when value="gff">
+ − 98 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
+ − 99 </when>
+ − 100 <when value="gff2">
+ − 101 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
+ − 102 </when>
+ − 103 <when value="gff3">
+ − 104 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
+ − 105 </when>
+ − 106 <when value="sam">
+ − 107 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
+ − 108 </when>
+ − 109 <when value="gtf">
+ − 110 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
+ − 111 </when>
+ − 112 </conditional>
+ − 113
+ − 114 <conditional name="formatType2">
+ − 115 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
+ − 116 <option value="bed">bed</option>
+ − 117 <option value="gff">gff</option>
+ − 118 <option value="gff2">gff2</option>
+ − 119 <option value="gff3">gff3</option>
+ − 120 <option value="sam">sam</option>
+ − 121 <option value="gtf">gtf</option>
+ − 122 </param>
+ − 123 <when value="bed">
+ − 124 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
+ − 125 </when>
+ − 126 <when value="gff">
+ − 127 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
+ − 128 </when>
+ − 129 <when value="gff2">
+ − 130 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
+ − 131 </when>
+ − 132 <when value="gff3">
+ − 133 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
+ − 134 </when>
+ − 135 <when value="sam">
+ − 136 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
+ − 137 </when>
+ − 138 <when value="gtf">
+ − 139 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
+ − 140 </when>
+ − 141 </conditional>
+ − 142
+ − 143 <param name="outputDistance" type="boolean" truevalue="-O" falsevalue="" checked="false" label="distance option" help="This option create a GFF3 output file containing the distance for each element of the query."/>
+ − 144
+ − 145 <param name="absolute" type="boolean" truevalue="-b" falsevalue="" checked="false" label="absolute value option" help="This option gives the absolute value of the distance."/>
+ − 146 <param name="proportion" type="boolean" truevalue="-p" falsevalue="" checked="false" label="proportion option" help="This option gives the proportion on the y-axis instead of the number of distances."/>
+ − 147
+ − 148 <conditional name="OptionColinearOrAntiSens">
+ − 149 <param name="OptionCA" type="select" label="Colinear or anti-sens">
+ − 150 <option value="Colinear">Colinear</option>
+ − 151 <option value="AntiSens">AntiSens</option>
+ − 152 <option value="NONE" selected="true">NONE</option>
+ − 153 </param>
+ − 154 <when value="Colinear">
+ − 155 </when>
+ − 156 <when value="AntiSens">
+ − 157 </when>
+ − 158 <when value="NONE">
+ − 159 </when>
+ − 160 </conditional>
+ − 161
+ − 162 <conditional name="OptionFirstNucl5">
+ − 163 <param name="FirstNu5" type="select" label="only consider the n first 5' nucleotides for input files">
+ − 164 <option value="Yes">Yes</option>
+ − 165 <option value="No" selected="true">No</option>
+ − 166 </param>
+ − 167 <when value="Yes">
+ − 168 <param name="first5File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/>
+ − 169 <param name="first5File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/>
+ − 170 </when>
+ − 171 <when value="No">
+ − 172 </when>
+ − 173 </conditional>
+ − 174
+ − 175 <conditional name="OptionFirstNucl3">
+ − 176 <param name="FirstNu3" type="select" label="only consider the n first 3' nucleotides for input files">
+ − 177 <option value="Yes">Yes</option>
+ − 178 <option value="No" selected="true">No</option>
+ − 179 </param>
+ − 180 <when value="Yes">
+ − 181 <param name="first3File1" type="integer" value="1" label="in file 1" help="Be Careful! The value must be upper than 0"/>
+ − 182 <param name="first3File2" type="integer" value="1" label="in file 2" help="Be Careful! The value must be upper than 0"/>
+ − 183 </when>
+ − 184 <when value="No">
+ − 185 </when>
+ − 186 </conditional>
+ − 187
+ − 188 <conditional name="OptionMinDistance">
+ − 189 <param name="MinD" type="select" label="minimum distance considered between two transcripts">
+ − 190 <option value="Yes">Yes</option>
+ − 191 <option value="No" selected="true">No</option>
+ − 192 </param>
+ − 193 <when value="Yes">
+ − 194 <param name="minDistance" type="integer" value="1"/>
+ − 195 </when>
+ − 196 <when value="No">
+ − 197 </when>
+ − 198 </conditional>
+ − 199
+ − 200 <conditional name="OptionMaxDistance">
+ − 201 <param name="MaxD" type="select" label="maximum distance considered between two transcripts">
+ − 202 <option value="Yes">Yes</option>
+ − 203 <option value="No" selected="true">No</option>
+ − 204 </param>
+ − 205 <when value="Yes">
+ − 206 <param name="maxDistance" type="integer" value="1000"/>
+ − 207 </when>
+ − 208 <when value="No">
+ − 209 </when>
+ − 210 </conditional>
+ − 211
+ − 212 <param name="fivePrime" type="boolean" truevalue="-5" falsevalue="" checked="false" label="five prime option" help="Consider the elements from input file 1 which are upstream of elements of input file 2"/>
+ − 213 <param name="threePrime" type="boolean" truevalue="-3" falsevalue="" checked="false" label="three prime option" help="Consider the elements from input file1 which are downstream of elements of input file 2"/>
+ − 214 <param name="spearMan" type="boolean" truevalue="-r" falsevalue="" checked="false" label="spearman option" help="Compute Spearman rho."/>
+ − 215
+ − 216
+ − 217 <conditional name="OptionBuckets">
+ − 218 <param name="OBuckets" type="select" label="Plots histogram instead of line plot with given interval size.">
+ − 219 <option value="Yes">Yes</option>
+ − 220 <option value="No" selected="true">No</option>
+ − 221 </param>
+ − 222 <when value="Yes">
+ − 223 <param name="buckets" type="integer" value="1" label="Interval size"/>
+ − 224 </when>
+ − 225 <when value="No">
+ − 226 </when>
+ − 227 </conditional>
+ − 228
+ − 229 <conditional name="OptionMinXaxis">
+ − 230 <param name="MinX" type="select" label="Minimum value on the x-axis to plot.">
+ − 231 <option value="Yes">Yes</option>
+ − 232 <option value="No" selected="true">No</option>
+ − 233 </param>
+ − 234 <when value="Yes">
+ − 235 <param name="minXaxis" type="integer" value="1"/>
+ − 236 </when>
+ − 237 <when value="No">
+ − 238 </when>
+ − 239 </conditional>
+ − 240
+ − 241 <conditional name="OptionMaxXaxis">
+ − 242 <param name="MaxX" type="select" label="Maximum value on the x-axis to plot.">
+ − 243 <option value="Yes">Yes</option>
+ − 244 <option value="No" selected="true">No</option>
+ − 245 </param>
+ − 246 <when value="Yes">
+ − 247 <param name="maxXaxis" type="integer" value="1"/>
+ − 248 </when>
+ − 249 <when value="No">
+ − 250 </when>
+ − 251 </conditional>
+ − 252
+ − 253 <conditional name="OptionTitle">
+ − 254 <param name="OTitle" type="select" label="Title for the graph.">
+ − 255 <option value="Yes">Yes</option>
+ − 256 <option value="No" selected="true">No</option>
+ − 257 </param>
+ − 258 <when value="Yes">
+ − 259 <param name="title" type="text" value=""/>
+ − 260 </when>
+ − 261 <when value="No">
+ − 262 </when>
+ − 263 </conditional>
+ − 264
+ − 265 </inputs>
+ − 266
+ − 267
+ − 268 <outputs>
+ − 269 <data name="outputFilePng" format="png"/>
+ − 270 <data name="outputFileDistance" format="gff3">
+ − 271 <filter>outputDistance</filter>
+ − 272 </data>
+ − 273 </outputs>
+ − 274
+ − 275 </tool>