Mercurial > repos > jtilman > flexbar
comparison flexbar.xml @ 20:83e3813084f2
Adjustment of when tags.
| author | jtilman |
|---|---|
| date | Tue, 21 May 2013 16:01:38 +0200 |
| parents | 621fa3daa2a1 |
| children | d62311a7bac6 |
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| 19:621fa3daa2a1 | 20:83e3813084f2 |
|---|---|
| 148 <conditional name="cReads2"> | 148 <conditional name="cReads2"> |
| 149 <param name="select" type="select" label="2nd read set (paired)"> | 149 <param name="select" type="select" label="2nd read set (paired)"> |
| 150 <option value="off" selected="true">Off</option> | 150 <option value="off" selected="true">Off</option> |
| 151 <option value="on">On</option> | 151 <option value="on">On</option> |
| 152 </param> | 152 </param> |
| 153 <when value="off"> | |
| 154 </when> | |
| 153 <when value="on"> | 155 <when value="on"> |
| 154 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/> | 156 <param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/> |
| 155 </when> | 157 </when> |
| 156 </conditional> | 158 </conditional> |
| 157 | 159 |
| 161 <conditional name="trimEnds"> | 163 <conditional name="trimEnds"> |
| 162 <param name="select" type="select" label="2) Trimming of ends"> | 164 <param name="select" type="select" label="2) Trimming of ends"> |
| 163 <option value="off" selected="true">Off</option> | 165 <option value="off" selected="true">Off</option> |
| 164 <option value="on">On</option> | 166 <option value="on">On</option> |
| 165 </param> | 167 </param> |
| 168 <when value="off"> | |
| 169 </when> | |
| 166 <when value="on"> | 170 <when value="on"> |
| 167 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/> | 171 <param name="trimLeft" size="4" type="integer" value="0" label="Left" optional="false"/> |
| 168 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/> | 172 <param name="trimRight" size="4" type="integer" value="0" label="Right" optional="false" help="trims specified number of bases from read ends"/> |
| 169 </when> | 173 </when> |
| 170 </conditional> | 174 </conditional> |
| 172 <conditional name="cTrimPhred"> | 176 <conditional name="cTrimPhred"> |
| 173 <param name="select" type="select" label="3) Phred-trimming"> | 177 <param name="select" type="select" label="3) Phred-trimming"> |
| 174 <option value="off" selected="true">Off</option> | 178 <option value="off" selected="true">Off</option> |
| 175 <option value="on">On</option> | 179 <option value="on">On</option> |
| 176 </param> | 180 </param> |
| 181 <when value="off"> | |
| 182 </when> | |
| 177 <when value="on"> | 183 <when value="on"> |
| 178 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/> | 184 <param name="trimPhred" size="4" type="integer" value="10" label="Threshold" optional="false" help="trim right end until specified or higher quality reached"/> |
| 179 </when> | 185 </when> |
| 180 </conditional> | 186 </conditional> |
| 181 | 187 |
| 183 <conditional name="cBarcodes"> | 189 <conditional name="cBarcodes"> |
| 184 <param name="select" type="select" label="4) Barcode detection"> | 190 <param name="select" type="select" label="4) Barcode detection"> |
| 185 <option value="off" selected="true">Off</option> | 191 <option value="off" selected="true">Off</option> |
| 186 <option value="on">On</option> | 192 <option value="on">On</option> |
| 187 </param> | 193 </param> |
| 194 <when value="off"> | |
| 195 </when> | |
| 188 <when value="on"> | 196 <when value="on"> |
| 189 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/> | 197 <param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/> |
| 190 <conditional name="cbReads"> | 198 <conditional name="cbReads"> |
| 191 <param name="select" type="select" label="Separate barcode reads"> | 199 <param name="select" type="select" label="Separate barcode reads"> |
| 192 <option value="no" selected="true">No</option> | 200 <option value="no" selected="true">No</option> |
| 212 <conditional name="cbTailLen"> | 220 <conditional name="cbTailLen"> |
| 213 <param name="select" type="select" label="Change tail length"> | 221 <param name="select" type="select" label="Change tail length"> |
| 214 <option value="no" selected="true">No</option> | 222 <option value="no" selected="true">No</option> |
| 215 <option value="yes">Yes</option> | 223 <option value="yes">Yes</option> |
| 216 </param> | 224 </param> |
| 225 <when value="no"> | |
| 226 </when> | |
| 217 <when value="yes"> | 227 <when value="yes"> |
| 218 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/> | 228 <param name="bTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/> |
| 219 </when> | 229 </when> |
| 220 </conditional> | 230 </conditional> |
| 221 | 231 |
| 222 <conditional name="cbMinOverlap"> | 232 <conditional name="cbMinOverlap"> |
| 223 <param name="select" type="select" label="Change min-overlap" help="default: barcode length"> | 233 <param name="select" type="select" label="Change min-overlap" help="default: barcode length"> |
| 224 <option value="no" selected="true">No</option> | 234 <option value="no" selected="true">No</option> |
| 225 <option value="yes">Yes</option> | 235 <option value="yes">Yes</option> |
| 226 </param> | 236 </param> |
| 237 <when value="no"> | |
| 238 </when> | |
| 227 <when value="yes"> | 239 <when value="yes"> |
| 228 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/> | 240 <param name="bMinOverlap" size="4" type="integer" value="8" label="Min-overlap" optional="false"/> |
| 229 </when> | 241 </when> |
| 230 </conditional> | 242 </conditional> |
| 231 | 243 |
| 234 <conditional name="cbAlignScores"> | 246 <conditional name="cbAlignScores"> |
| 235 <param name="select" type="select" label="Modify alignment scores"> | 247 <param name="select" type="select" label="Modify alignment scores"> |
| 236 <option value="no" selected="true">No</option> | 248 <option value="no" selected="true">No</option> |
| 237 <option value="yes">Yes</option> | 249 <option value="yes">Yes</option> |
| 238 </param> | 250 </param> |
| 251 <when value="no"> | |
| 252 </when> | |
| 239 <when value="yes"> | 253 <when value="yes"> |
| 240 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/> | 254 <param name="bMatch" size="3" type="integer" value="1" label="Match" optional="false"/> |
| 241 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/> | 255 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/> |
| 242 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/> | 256 <param name="bGap" size="3" type="integer" value="-7" label="Gap" optional="false"/> |
| 243 </when> | 257 </when> |
| 250 <param name="select" type="select" label="5) Adapter removal"> | 264 <param name="select" type="select" label="5) Adapter removal"> |
| 251 <option value="off" selected="true">Off</option> | 265 <option value="off" selected="true">Off</option> |
| 252 <option value="on">On</option> | 266 <option value="on">On</option> |
| 253 </param> | 267 </param> |
| 254 | 268 |
| 269 <when value="off"> | |
| 270 </when> | |
| 255 <when value="on"> | 271 <when value="on"> |
| 256 <conditional name="ccAdapters"> | 272 <conditional name="ccAdapters"> |
| 257 <param name="select" type="select" label="Adapter source"> | 273 <param name="select" type="select" label="Adapter source"> |
| 258 <option value="data" selected="true">Fasta</option> | 274 <option value="data" selected="true">Fasta</option> |
| 259 <option value="seq">Sequence</option> | 275 <option value="seq">Sequence</option> |
| 281 <conditional name="caTailLen"> | 297 <conditional name="caTailLen"> |
| 282 <param name="select" type="select" label="Change tail length"> | 298 <param name="select" type="select" label="Change tail length"> |
| 283 <option value="no" selected="true">No</option> | 299 <option value="no" selected="true">No</option> |
| 284 <option value="yes">Yes</option> | 300 <option value="yes">Yes</option> |
| 285 </param> | 301 </param> |
| 302 <when value="no"> | |
| 303 </when> | |
| 286 <when value="yes"> | 304 <when value="yes"> |
| 287 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/> | 305 <param name="aTailLen" size="4" type="integer" value="10" label="Tail length" optional="false"/> |
| 288 </when> | 306 </when> |
| 289 </conditional> | 307 </conditional> |
| 290 | 308 |
| 294 <conditional name="caAlignScores"> | 312 <conditional name="caAlignScores"> |
| 295 <param name="select" type="select" label="Modify alignment scores"> | 313 <param name="select" type="select" label="Modify alignment scores"> |
| 296 <option value="no" selected="true">No</option> | 314 <option value="no" selected="true">No</option> |
| 297 <option value="yes">Yes</option> | 315 <option value="yes">Yes</option> |
| 298 </param> | 316 </param> |
| 317 <when value="no"> | |
| 318 </when> | |
| 299 <when value="yes"> | 319 <when value="yes"> |
| 300 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/> | 320 <param name="aMatch" size="3" type="integer" value="1" label="Match" optional="false"/> |
| 301 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/> | 321 <param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/> |
| 302 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/> | 322 <param name="aGap" size="3" type="integer" value="-7" label="Gap" optional="false"/> |
| 303 </when> | 323 </when> |
| 309 <conditional name="cTrimLen"> | 329 <conditional name="cTrimLen"> |
| 310 <param name="select" type="select" label="6) Trimming to length"> | 330 <param name="select" type="select" label="6) Trimming to length"> |
| 311 <option value="off" selected="true">Off</option> | 331 <option value="off" selected="true">Off</option> |
| 312 <option value="on">On</option> | 332 <option value="on">On</option> |
| 313 </param> | 333 </param> |
| 334 <when value="off"> | |
| 335 </when> | |
| 314 <when value="on"> | 336 <when value="on"> |
| 315 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/> | 337 <param name="trimLen" size="4" type="integer" value="30" label="Length" optional="false" help="trim reads to certain length from right"/> |
| 316 </when> | 338 </when> |
| 317 </conditional> | 339 </conditional> |
| 318 | 340 |
| 322 <conditional name="cLogging"> | 344 <conditional name="cLogging"> |
| 323 <param name="select" type="select" label="Logging and tagging options"> | 345 <param name="select" type="select" label="Logging and tagging options"> |
| 324 <option value="off" selected="true">Off</option> | 346 <option value="off" selected="true">Off</option> |
| 325 <option value="show">Show</option> | 347 <option value="show">Show</option> |
| 326 </param> | 348 </param> |
| 349 <when value="off"> | |
| 350 </when> | |
| 327 <when value="show"> | 351 <when value="show"> |
| 328 <param name="logLevel" type="select" label="Alignment logging"> | 352 <param name="logLevel" type="select" label="Alignment logging"> |
| 329 <option value="" selected="true">Off</option> | 353 <option value="" selected="true">Off</option> |
| 330 <option value="--log-level ALL">All</option> | 354 <option value="--log-level ALL">All</option> |
| 331 <option value="--log-level MOD">Modified</option> | 355 <option value="--log-level MOD">Modified</option> |