Mercurial > repos > bjoern-gruening > bismark
comparison bismark_bowtie_wrapper.xml @ 4:427fb56f2e41 draft default tip
- new options
- fixes
author | bjoern-gruening |
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date | Fri, 01 Mar 2013 13:39:22 -0500 |
parents | 36d124f44c0a |
children |
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3:7eefe5d6eecd | 4:427fb56f2e41 |
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1 <tool id="bismark_bowtie" name="Bismark" version="0.7.7.2"> | 1 <tool id="bismark_bowtie" name="Bismark" version="0.7.7.3"> |
2 <!-- Wrapper compatible with Bismark version 0.7.7 --> | 2 <!-- Wrapper compatible with Bismark version 0.7.7 --> |
3 <description>bisulfite mapper (bowtie)</description> | 3 <description>bisulfite mapper (bowtie)</description> |
4 <!--<version_command>bismark version</version_command>--> | 4 <!--<version_command>bismark version</version_command>--> |
5 <requirements> | 5 <requirements> |
6 <requirement type="set_environment">SCRIPT_PATH</requirement> | 6 <requirement type="set_environment">SCRIPT_PATH</requirement> |
8 <requirement type="package" version="2.0.0-beta7">bowtie2</requirement> | 8 <requirement type="package" version="2.0.0-beta7">bowtie2</requirement> |
9 </requirements> | 9 </requirements> |
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 | |
14 ## Change this to accommodate the number of threads you have available. | |
15 --num-threads 4 | |
16 | 13 |
17 --bismark_path \$SCRIPT_PATH | 14 --bismark_path \$SCRIPT_PATH |
18 | 15 |
19 ## | 16 ## |
20 ## Bismark Genome Preparation, if desired. | 17 ## Bismark Genome Preparation, if desired. |
43 --fastq | 40 --fastq |
44 #elif $singlePaired.input_singles.ext == "fasta": | 41 #elif $singlePaired.input_singles.ext == "fasta": |
45 --fasta | 42 --fasta |
46 #end if | 43 #end if |
47 #else: | 44 #else: |
48 --mate-paired | 45 --mate-paired |
49 --mate1 $singlePaired.input_mate1 | 46 #set $mate1 = list() |
50 --mate2 $singlePaired.input_mate2 | 47 #set $mate2 = list() |
51 | 48 #for $mate_pair in $singlePaired.mate_list |
52 #if $singlePaired.input_mate1.ext == "fastqillumina": | 49 $mate1.append( str($mate_pair.input_mate1) ) |
50 $mate2.append( str($mate_pair.input_mate2) ) | |
51 #end for | |
52 | |
53 --mate1 #echo ','.join($mate1) | |
54 --mate2 #echo ','.join($mate2) | |
55 | |
56 #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina": | |
53 --phred64-quals | 57 --phred64-quals |
54 --fastq | 58 --fastq |
55 #elif $singlePaired.input_mate1.ext == "fastqsanger": | 59 #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger": |
56 --fastq | 60 --fastq |
57 #elif $singlePaired.input_mate1.ext == "fasta": | 61 #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta": |
58 --fasta | 62 --fasta |
59 #end if | 63 #end if |
60 | 64 |
61 -I $singlePaired.minInsert | 65 -I $singlePaired.minInsert |
62 -X $singlePaired.maxInsert | 66 -X $singlePaired.maxInsert |
71 | 75 |
72 ## default 20 | 76 ## default 20 |
73 --seed-len $params.seed_len | 77 --seed-len $params.seed_len |
74 ## default 0 | 78 ## default 0 |
75 --seed-mismatches $params.seed_mismatches | 79 --seed-mismatches $params.seed_mismatches |
76 ## default 15 | 80 |
77 --seed-extention-attempts $params.seed_extention_attempts | |
78 ## default 2 | |
79 --max-reseed $params.max_reseed | |
80 | |
81 ## default 70 | 81 ## default 70 |
82 ##--maqerr $params.maqerr | 82 ##--maqerr $params.maqerr |
83 | 83 |
84 ## default unlimited | 84 ## default unlimited |
85 #if $params.qupto != 0: | 85 #if $params.qupto != 0: |
86 --qupto $params.qupto | 86 --qupto $params.qupto |
87 #end if | 87 #end if |
88 #if $params.skip_reads != 0: | 88 #if $params.skip_reads != 0: |
89 --skip-reads $params.skip_reads | 89 --skip-reads $params.skip_reads |
90 #end if | 90 #end if |
91 | |
92 ## if set, disable the original behaviour | |
93 $params.no_mixed | |
94 ## if set, disable the original behaviour | |
95 $params.no_discordant | |
96 | |
97 | 91 |
98 ###if str($params.isReportOutput) == "yes": | 92 ###if str($params.isReportOutput) == "yes": |
99 ## --output-report-file $report_file | 93 ## --output-report-file $report_file |
100 ###end if | 94 ###end if |
101 | 95 |
153 </param> | 147 </param> |
154 <when value="single"> | 148 <when value="single"> |
155 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> | 149 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> |
156 </when> | 150 </when> |
157 <when value="paired"> | 151 <when value="paired"> |
158 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> | 152 <repeat name="mate_list" title="Paired End Pairs" min="1"> |
159 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." /> | 153 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." /> |
154 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." /> | |
155 </repeat> | |
160 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> | 156 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> |
161 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /> | 157 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" /> |
162 </when> | 158 </when> |
163 </conditional> | 159 </conditional> |
164 | 160 |
183 <!-- | 179 <!-- |
184 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." /> | 180 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." /> |
185 --> | 181 --> |
186 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." /> | 182 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." /> |
187 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" /> | 183 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" /> |
188 | |
189 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" /> | |
190 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" /> | |
191 | 184 |
192 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." /> | 185 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." /> |
193 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" /> | 186 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" /> |
194 <!-- output Options --> | 187 <!-- output Options --> |
195 <!-- | 188 <!-- |
243 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 236 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
244 </action> | 237 </action> |
245 </when> | 238 </when> |
246 <when value="paired"> | 239 <when value="paired"> |
247 <action type="format"> | 240 <action type="format"> |
248 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 241 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
249 </action> | 242 </action> |
250 </when> | 243 </when> |
251 </conditional> | 244 </conditional> |
252 </actions> | 245 </actions> |
253 </data> | 246 </data> |
263 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 256 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
264 </action> | 257 </action> |
265 </when> | 258 </when> |
266 <when value="paired"> | 259 <when value="paired"> |
267 <action type="format"> | 260 <action type="format"> |
268 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 261 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
269 </action> | 262 </action> |
270 </when> | 263 </when> |
271 </conditional> | 264 </conditional> |
272 </actions> | 265 </actions> |
273 </data> | 266 </data> |
287 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 280 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
288 </action> | 281 </action> |
289 </when> | 282 </when> |
290 <when value="paired"> | 283 <when value="paired"> |
291 <action type="format"> | 284 <action type="format"> |
292 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 285 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
293 </action> | 286 </action> |
294 </when> | 287 </when> |
295 </conditional> | 288 </conditional> |
296 </actions> | 289 </actions> |
297 </data> | 290 </data> |
306 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> | 299 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> |
307 </action> | 300 </action> |
308 </when> | 301 </when> |
309 <when value="paired"> | 302 <when value="paired"> |
310 <action type="format"> | 303 <action type="format"> |
311 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" /> | 304 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> |
312 </action> | 305 </action> |
313 </when> | 306 </when> |
314 </conditional> | 307 </conditional> |
315 </actions> | 308 </actions> |
316 </data> | 309 </data> |
348 .. class:: warningmark | 341 .. class:: warningmark |
349 | 342 |
350 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. | 343 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. |
351 | 344 |
352 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ | 345 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
346 | |
347 | |
348 .. class:: warningmark | |
349 | |
350 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. | |
353 | 351 |
354 ------ | 352 ------ |
355 | 353 |
356 **Input formats** | 354 **Input formats** |
357 | 355 |
411 | 409 |
412 ------ | 410 ------ |
413 | 411 |
414 **Bismark parameter list** | 412 **Bismark parameter list** |
415 | 413 |
416 This is an exhaustive list of Bismark options: | 414 This is an exhaustive list of Bismark options. |
417 | |
418 ------ | |
419 | |
420 **OPTIONS** | |
421 | |
422 | 415 |
423 Input:: | 416 Input:: |
424 | 417 |
425 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g. | 418 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g. |
426 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will | 419 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will |
537 | 530 |
538 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If | 531 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If |
539 the specified folder does not exist, Bismark will attempt to create it first. The path to the | 532 the specified folder does not exist, Bismark will attempt to create it first. The path to the |
540 temporary folder can be either relative or absolute. | 533 temporary folder can be either relative or absolute. |
541 | 534 |
542 ------ | |
543 | |
544 Bowtie 2 alignment options:: | |
545 | |
546 -N INT Sets the number of mismatches to allowed in a seed alignment during multiseed alignment. | |
547 Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) | |
548 but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for | |
549 Bowtie 1 see -n). | |
550 | |
551 -L INT Sets the length of the seed substrings to align during multiseed alignment. Smaller values | |
552 make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is | |
553 used by default, which sets -L to 20. This option is only available for Bowtie 2 (for | |
554 Bowtie 1 see -l). | |
555 | |
556 --ignore-quals When calculating a mismatch penalty, always consider the quality value at the mismatched | |
557 position to be the highest possible, regardless of the actual value. I.e. input is treated | |
558 as though all quality values are high. This is also the default behavior when the input | |
559 doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default. | |
560 | |
561 | |
562 Bowtie 2 paired-end options:: | |
563 | |
564 --no-mixed This option disables Bowtie 2's behavior to try to find alignments for the individual mates if | |
565 it cannot find a concordant or discordant alignment for a pair. This option is invariable and | |
566 and on by default. | |
567 | |
568 --no-discordant Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments. | |
569 A discordant alignment is an alignment where both mates align uniquely, but that does not | |
570 satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior | |
571 and it is on by default. | |
572 | |
573 | |
574 Bowtie 2 effort options:: | |
575 | |
576 -D INT Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using | |
577 the alignments found so far. A seed extension "fails" if it does not yield a new best or a | |
578 new second-best alignment. Default: 15. | |
579 | |
580 -R INT INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds. | |
581 When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of | |
582 mismatches allowed) at different offsets and searches for more alignments. A read is considered | |
583 to have repetitive seeds if the total number of seed hits divided by the number of seeds | |
584 that aligned at least once is greater than 300. Default: 2. | |
585 | |
586 | |
587 Bowtie 2 Scoring options:: | |
588 | |
589 --score_min "func" Sets a function governing the minimum alignment score needed for an alignment to be considered | |
590 "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying | |
591 L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length. | |
592 See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is | |
593 L,0,-0.2. | |
594 | |
595 | |
596 Bowtie 2 Reporting options:: | |
597 | |
598 --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is | |
599 deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the | |
600 default mode, but adjusting the -M setting is deprecated. Use the -D and -R options to adjust the | |
601 effort expended to find valid alignments. | |
602 | |
603 For reference, this used to be the old (now deprecated) description of -M: | |
604 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it | |
605 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever | |
606 happens first. Only the best alignment is reported. Information from the other alignments is used to | |
607 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes | |
608 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that | |
609 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not | |
610 guarantee that the alignment reported is the best possible in terms of alignment score. -M is | |
611 always used and its default value is set to 10. | |
612 | |
613 </help> | 535 </help> |
614 </tool> | 536 </tool> |