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comparison bismark_bowtie2_wrapper.xml @ 4:427fb56f2e41 draft default tip

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- new options - fixes
author bjoern-gruening
date Fri, 01 Mar 2013 13:39:22 -0500
parents 36d124f44c0a
children
comparison
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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