Mercurial > repos > bjoern-gruening > bismark
comparison bismark_bowtie2_wrapper.xml @ 4:427fb56f2e41 draft default tip
- new options
- fixes
| author | bjoern-gruening |
|---|---|
| date | Fri, 01 Mar 2013 13:39:22 -0500 |
| parents | 36d124f44c0a |
| children |
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| 3:7eefe5d6eecd | 4:427fb56f2e41 |
|---|---|
| 10 <parallelism method="basic"></parallelism> | 10 <parallelism method="basic"></parallelism> |
| 11 <command interpreter="python"> | 11 <command interpreter="python"> |
| 12 bismark_wrapper.py | 12 bismark_wrapper.py |
| 13 | 13 |
| 14 ## Change this to accommodate the number of threads you have available. | 14 ## Change this to accommodate the number of threads you have available. |
| 15 --num-threads 4 | 15 --num-threads 12 |
| 16 | 16 |
| 17 --bismark_path \$SCRIPT_PATH | 17 --bismark_path \$SCRIPT_PATH |
| 18 | 18 |
| 19 --bowtie2 | 19 --bowtie2 |
| 20 | 20 |
| 45 --fastq | 45 --fastq |
| 46 #elif $singlePaired.input_singles.ext == "fasta": | 46 #elif $singlePaired.input_singles.ext == "fasta": |
| 47 --fasta | 47 --fasta |
| 48 #end if | 48 #end if |
| 49 #else: | 49 #else: |
| 50 --mate-paired | 50 --mate-paired |
| 51 --mate1 $singlePaired.input_mate1 | 51 #set $mate1 = list() |
| 52 --mate2 $singlePaired.input_mate2 | 52 #set $mate2 = list() |
| 53 | 53 #for $mate_pair in $singlePaired.mate_list |
| 54 #if $singlePaired.input_mate1.ext == "fastqillumina": | 54 $mate1.append( str($mate_pair.input_mate1) ) |
| 55 $mate2.append( str($mate_pair.input_mate2) ) | |
| 56 #end for | |
| 57 | |
| 58 --mate1 #echo ','.join($mate1) | |
| 59 --mate2 #echo ','.join($mate2) | |
| 60 | |
| 61 #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina": | |
| 55 --phred64-quals | 62 --phred64-quals |
| 56 --fastq | 63 --fastq |
| 57 #elif $singlePaired.input_mate1.ext == "fastqsanger": | 64 #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger": |
| 58 --fastq | 65 --fastq |
| 59 #elif $singlePaired.input_mate1.ext == "fasta": | 66 #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta": |
| 60 --fasta | 67 --fasta |
| 61 #end if | 68 #end if |
| 62 | 69 |
| 63 -I $singlePaired.minInsert | 70 -I $singlePaired.minInsert |
| 64 -X $singlePaired.maxInsert | 71 -X $singlePaired.maxInsert |
| 155 </param> | 162 </param> |
| 156 <when value="single"> | 163 <when value="single"> |
| 157 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> | 164 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> |
| 158 </when> | 165 </when> |
| 159 <when value="paired"> | 166 <when value="paired"> |
| 160 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> | 167 <repeat name="mate_list" title="Paired End Pairs" min="1"> |
| 161 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> | 168 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." /> |
| 169 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." /> | |
| 170 </repeat> | |
| 162 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> | 171 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> |
| 163 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /> | 172 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /> |
| 164 </when> | 173 </when> |
| 165 </conditional> | 174 </conditional> |
| 166 | 175 |
| 245 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 254 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 246 </action> | 255 </action> |
| 247 </when> | 256 </when> |
| 248 <when value="paired"> | 257 <when value="paired"> |
| 249 <action type="format"> | 258 <action type="format"> |
| 250 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 259 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 251 </action> | 260 </action> |
| 252 </when> | 261 </when> |
| 253 </conditional> | 262 </conditional> |
| 254 </actions> | 263 </actions> |
| 255 </data> | 264 </data> |
| 265 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 274 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 266 </action> | 275 </action> |
| 267 </when> | 276 </when> |
| 268 <when value="paired"> | 277 <when value="paired"> |
| 269 <action type="format"> | 278 <action type="format"> |
| 270 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 279 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 271 </action> | 280 </action> |
| 272 </when> | 281 </when> |
| 273 </conditional> | 282 </conditional> |
| 274 </actions> | 283 </actions> |
| 275 </data> | 284 </data> |
| 289 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 298 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 290 </action> | 299 </action> |
| 291 </when> | 300 </when> |
| 292 <when value="paired"> | 301 <when value="paired"> |
| 293 <action type="format"> | 302 <action type="format"> |
| 294 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 303 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 295 </action> | 304 </action> |
| 296 </when> | 305 </when> |
| 297 </conditional> | 306 </conditional> |
| 298 </actions> | 307 </actions> |
| 299 </data> | 308 </data> |
| 308 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 317 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 309 </action> | 318 </action> |
| 310 </when> | 319 </when> |
| 311 <when value="paired"> | 320 <when value="paired"> |
| 312 <action type="format"> | 321 <action type="format"> |
| 313 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 322 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 314 </action> | 323 </action> |
| 315 </when> | 324 </when> |
| 316 </conditional> | 325 </conditional> |
| 317 </actions> | 326 </actions> |
| 318 </data> | 327 </data> |
| 350 .. class:: warningmark | 359 .. class:: warningmark |
| 351 | 360 |
| 352 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. | 361 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. |
| 353 | 362 |
| 354 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ | 363 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| 364 | |
| 365 | |
| 366 .. class:: warningmark | |
| 367 | |
| 368 Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters. | |
| 355 | 369 |
| 356 ------ | 370 ------ |
| 357 | 371 |
| 358 **Input formats** | 372 **Input formats** |
| 359 | 373 |
| 413 | 427 |
| 414 ------ | 428 ------ |
| 415 | 429 |
| 416 **Bismark parameter list** | 430 **Bismark parameter list** |
| 417 | 431 |
| 418 This is an exhaustive list of Bismark options: | 432 This is an exhaustive list of Bismark options. |
| 419 | |
| 420 ------ | |
| 421 | |
| 422 **OPTIONS** | |
| 423 | |
| 424 | 433 |
| 425 Input:: | 434 Input:: |
| 426 | 435 |
| 427 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g. | 436 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g. |
| 428 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will | 437 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will |