Mercurial > repos > bgruening > bismark
comparison bismark_bowtie_wrapper.xml @ 20:0895fe70075d draft
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 26 Jan 2015 14:46:05 -0500 |
| parents | 30caca800c9b |
| children | 507901240749 |
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| 19:30caca800c9b | 20:0895fe70075d |
|---|---|
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="set_environment">SCRIPT_PATH</requirement> | 6 <requirement type="set_environment">SCRIPT_PATH</requirement> |
| 7 <requirement type="package" version="0.1.19">samtools</requirement> | 7 <requirement type="package" version="0.1.19">samtools</requirement> |
| 8 <requirement type="package" version="0.12.8">bowtie</requirement> | 8 <requirement type="package" version="0.12.8">bowtie</requirement> |
| 9 </requirements> | 9 </requirements> |
| 10 <stdio> | 10 <parallelism method="basic"></parallelism> |
| 11 <exit_code range="1:" /> | |
| 12 <exit_code range=":-1" /> | |
| 13 <regex match="Error:" /> | |
| 14 <regex match="Exception:" /> | |
| 15 </stdio> | |
| 16 <command interpreter="python"> | 11 <command interpreter="python"> |
| 17 bismark_wrapper.py | 12 bismark_wrapper.py |
| 18 | 13 |
| 19 ##--bismark_path \$SCRIPT_PATH | 14 --bismark_path \$SCRIPT_PATH |
| 20 | 15 |
| 21 ## | 16 ## |
| 22 ## Bismark Genome Preparation, if desired. | 17 ## Bismark Genome Preparation, if desired. |
| 23 ## | 18 ## |
| 24 | 19 |
| 56 #end for | 51 #end for |
| 57 | 52 |
| 58 --mate1 #echo ','.join($mate1) | 53 --mate1 #echo ','.join($mate1) |
| 59 --mate2 #echo ','.join($mate2) | 54 --mate2 #echo ','.join($mate2) |
| 60 | 55 |
| 61 #for $mate_pair in $singlePaired.mate_list: | 56 #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina": |
| 62 #if $mate_pair.input_mate1.ext == "fastqillumina": | 57 --phred64-quals |
| 63 --phred64-quals | 58 --fastq |
| 64 --fastq | 59 #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger": |
| 65 #elif $mate_pair.input_mate1.ext == "fastqsanger": | 60 --fastq |
| 66 --fastq | 61 #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta": |
| 67 #elif $mate_pair.input_mate1.ext == "fasta": | 62 --fasta |
| 68 --fasta | 63 #end if |
| 69 #end if | |
| 70 #break | |
| 71 #end for | |
| 72 | 64 |
| 73 -I $singlePaired.minInsert | 65 -I $singlePaired.minInsert |
| 74 -X $singlePaired.maxInsert | 66 -X $singlePaired.maxInsert |
| 75 #end if | 67 #end if |
| 76 | 68 |
| 257 <action type="format"> | 249 <action type="format"> |
| 258 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 250 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 259 </action> | 251 </action> |
| 260 </when> | 252 </when> |
| 261 <when value="paired"> | 253 <when value="paired"> |
| 262 <!--action type="format"> | 254 <action type="format"> |
| 263 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> | 255 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 264 </action--> | 256 </action> |
| 265 </when> | 257 </when> |
| 266 </conditional> | 258 </conditional> |
| 267 </actions> | 259 </actions> |
| 268 </data> | 260 </data> |
| 269 | 261 |
| 277 <action type="format"> | 269 <action type="format"> |
| 278 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 270 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 279 </action> | 271 </action> |
| 280 </when> | 272 </when> |
| 281 <when value="paired"> | 273 <when value="paired"> |
| 282 <!--action type="format"> | 274 <action type="format"> |
| 283 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> | 275 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 284 </action--> | 276 </action> |
| 285 </when> | 277 </when> |
| 286 </conditional> | 278 </conditional> |
| 287 </actions> | 279 </actions> |
| 288 </data> | 280 </data> |
| 289 | 281 |
| 301 <action type="format"> | 293 <action type="format"> |
| 302 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 294 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 303 </action> | 295 </action> |
| 304 </when> | 296 </when> |
| 305 <when value="paired"> | 297 <when value="paired"> |
| 306 <!--action type="format"> | 298 <action type="format"> |
| 307 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> | 299 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 308 </action--> | 300 </action> |
| 309 </when> | 301 </when> |
| 310 </conditional> | 302 </conditional> |
| 311 </actions> | 303 </actions> |
| 312 </data> | 304 </data> |
| 313 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> | 305 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> |
| 320 <action type="format"> | 312 <action type="format"> |
| 321 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 313 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
| 322 </action> | 314 </action> |
| 323 </when> | 315 </when> |
| 324 <when value="paired"> | 316 <when value="paired"> |
| 325 <!--action type="format"> | 317 <action type="format"> |
| 326 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> | 318 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
| 327 </action--> | 319 </action> |
| 328 </when> | 320 </when> |
| 329 </conditional> | 321 </conditional> |
| 330 </actions> | 322 </actions> |
| 331 </data> | 323 </data> |
| 324 | |
| 325 | |
| 332 </outputs> | 326 </outputs> |
| 333 | 327 |
| 334 <tests> | 328 <tests> |
| 335 </tests> | 329 </tests> |
| 336 | 330 |
| 551 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If | 545 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If |
| 552 the specified folder does not exist, Bismark will attempt to create it first. The path to the | 546 the specified folder does not exist, Bismark will attempt to create it first. The path to the |
| 553 temporary folder can be either relative or absolute. | 547 temporary folder can be either relative or absolute. |
| 554 | 548 |
| 555 </help> | 549 </help> |
| 556 <citations> | |
| 557 <citation type="doi">10.1093/bioinformatics/btr167</citation> | |
| 558 </citations> | |
| 559 </tool> | 550 </tool> |