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comparison bismark_bowtie2_wrapper.xml @ 4:243e8f9fb75b draft

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author bgruening
date Mon, 09 Feb 2015 18:24:41 -0500
parents 91f07ff056ca
children b100248c35b8
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3:91f07ff056ca 4:243e8f9fb75b
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="2.1.0">bowtie2</requirement> 8 <requirement type="package" version="2.1.0">bowtie2</requirement>
9 </requirements> 9 </requirements>
10 <parallelism method="basic"></parallelism> 10 <stdio>
11 <exit_code range="1:" />
12 <exit_code range=":-1" />
13 <regex match="Error:" />
14 <regex match="Exception:" />
15 </stdio>
11 <command interpreter="python"> 16 <command interpreter="python">
17 <![CDATA[
12 bismark_wrapper.py 18 bismark_wrapper.py
13 19
14 ## Change this to accommodate the number of threads you have available. 20 ## Change this to accommodate the number of threads you have available.
15 --num-threads "\${GALAXY_SLOTS:-24}" 21 --num-threads "\${GALAXY_SLOTS:-24}"
16 22
17 --bismark_path \$SCRIPT_PATH 23 ##--bismark_path \$SCRIPT_PATH
18 24
19 --bowtie2 25 --bowtie2
20 26
21 ## 27 ##
22 ## Bismark Genome Preparation, if desired. 28 ## Bismark Genome Preparation, if desired.
31 37
32 38
33 ## 39 ##
34 ## Input parameters 40 ## Input parameters
35 ## 41 ##
36
37 42
38 #if $singlePaired.sPaired == "single": 43 #if $singlePaired.sPaired == "single":
39 --single-paired $singlePaired.input_singles 44 --single-paired $singlePaired.input_singles
40 45
41 #if $singlePaired.input_singles.ext == "fastqillumina": 46 #if $singlePaired.input_singles.ext == "fastqillumina":
56 #end for 61 #end for
57 62
58 --mate1 #echo ','.join($mate1) 63 --mate1 #echo ','.join($mate1)
59 --mate2 #echo ','.join($mate2) 64 --mate2 #echo ','.join($mate2)
60 65
61 #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina": 66 #for $mate_pair in $singlePaired.mate_list:
62 --phred64-quals 67 #if $mate_pair.input_mate1.ext == "fastqillumina":
63 --fastq 68 --phred64-quals
64 #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger": 69 --fastq
65 --fastq 70 #elif $mate_pair.input_mate1.ext == "fastqsanger":
66 #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta": 71 --fastq
67 --fasta 72 #elif $mate_pair.input_mate1.ext == "fasta":
68 #end if 73 --fasta
74 #end if
75 #break
76 #end for
69 77
70 -I $singlePaired.minInsert 78 -I $singlePaired.minInsert
71 -X $singlePaired.maxInsert 79 -X $singlePaired.maxInsert
72 #end if 80 #end if
73 81
87 --seed-mismatches $params.seed_mismatches 95 --seed-mismatches $params.seed_mismatches
88 ## default 15 96 ## default 15
89 --seed-extention-attempts $params.seed_extention_attempts 97 --seed-extention-attempts $params.seed_extention_attempts
90 ## default 2 98 ## default 2
91 --max-reseed $params.max_reseed 99 --max-reseed $params.max_reseed
92 100
93 ## default 70 101 ## default 70
94 ##--maqerr $params.maqerr 102 ##--maqerr $params.maqerr
95 103
96 ## default unlimited 104 ## default unlimited
97 #if $params.qupto != 0: 105 #if $params.qupto != 0:
138 --output-suppressed-reads-l $output_suppressed_reads_l 146 --output-suppressed-reads-l $output_suppressed_reads_l
139 --output-suppressed-reads-r $output_suppressed_reads_r 147 --output-suppressed-reads-r $output_suppressed_reads_r
140 #end if 148 #end if
141 #end if 149 #end if
142 150
151 ]]>
143 </command> 152 </command>
144 <inputs> 153 <inputs>
145 <conditional name="refGenomeSource"> 154 <conditional name="refGenomeSource">
146 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 155 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
147 <option value="indexed">Use a built-in index</option> 156 <option value="indexed">Use a built-in index</option>
211 <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" /> 220 <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" />
212 <!-- output Options --> 221 <!-- output Options -->
213 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" /> 222 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
214 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" /> 223 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
215 224
216 <!--end output options --> 225 <!--end output options -->
217 </when> <!-- full --> 226 </when> <!-- full -->
218 </conditional> <!-- params --> 227 </conditional> <!-- params -->
219 <!-- 228 <!--
220 <param name="suppress_header" type="boolean" truevalue="..suppress-header" falsevalue="" checked="false" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default." /> 229 <param name="suppress_header" type="boolean" truevalue="..suppress-header" falsevalue="" checked="false" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default." />
221 --> 230 -->
273 <action type="format"> 282 <action type="format">
274 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 283 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
275 </action> 284 </action>
276 </when> 285 </when>
277 <when value="paired"> 286 <when value="paired">
278 <action type="format"> 287 <!--action type="format">
279 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 288 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
280 </action> 289 </action-->
281 </when> 290 </when>
282 </conditional> 291 </conditional>
283 </actions> 292 </actions>
284 </data> 293 </data>
285 294
286 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> 295 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
287 <filter>singlePaired['sPaired'] == "paired"</filter> 296 <filter>
288 <filter>params['settingsType'] == "custom"</filter> 297 ((
289 <filter>params['supressed_read_file'] is True</filter> 298 singlePaired['sPaired'] == "paired" and
299 params['settingsType'] == "custom" and
300 params['suppressed_read_file'] is True
301 ))
302 </filter>
290 <actions> 303 <actions>
291 <conditional name="singlePaired.sPaired"> 304 <conditional name="singlePaired.sPaired">
292 <when value="single"> 305 <when value="single">
293 <action type="format"> 306 <action type="format">
294 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 307 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
295 </action> 308 </action>
296 </when> 309 </when>
297 <when value="paired"> 310 <when value="paired">
298 <action type="format"> 311 <!--action type="format">
299 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 312 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
300 </action> 313 </action-->
301 </when> 314 </when>
302 </conditional> 315 </conditional>
303 </actions> 316 </actions>
304 </data> 317 </data>
305 318
317 <action type="format"> 330 <action type="format">
318 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 331 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
319 </action> 332 </action>
320 </when> 333 </when>
321 <when value="paired"> 334 <when value="paired">
322 <action type="format"> 335 <!--action type="format">
323 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 336 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
324 </action> 337 </action-->
325 </when> 338 </when>
326 </conditional> 339 </conditional>
327 </actions> 340 </actions>
328 </data> 341 </data>
329 342
330 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> 343 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
331 <filter>singlePaired['sPaired'] == "paired"</filter> 344 <filter>
332 <filter>params['settingsType'] == "custom"</filter> 345 ((
333 <filter>params['unmapped_read_file'] is True</filter> 346 singlePaired['sPaired'] == "paired" and
347 params['settingsType'] == "custom" and
348 params['unmapped_read_file'] is True
349 ))
350 </filter>
334 <actions> 351 <actions>
335 <conditional name="singlePaired.sPaired"> 352 <conditional name="singlePaired.sPaired">
336 <when value="single"> 353 <when value="single">
337 <action type="format"> 354 <action type="format">
338 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 355 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
339 </action> 356 </action>
340 </when> 357 </when>
341 <when value="paired"> 358 <when value="paired">
342 <action type="format"> 359 <!--action type="format">
343 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 360 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
344 </action> 361 </action-->
345 </when> 362 </when>
346 </conditional> 363 </conditional>
347 </actions> 364 </actions>
348 </data> 365 </data>
349 </outputs> 366 </outputs>
350 367
351 <tests> 368 <tests>
352 </tests> 369 </tests>
353 370
354 <help> 371 <help>
372 <![CDATA[
355 373
356 **What it does** 374 **What it does**
357 375
358 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the 376 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
359 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand 377 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
407 The output is in SAM format, and has the following columns:: 425 The output is in SAM format, and has the following columns::
408 426
409 Column Description 427 Column Description
410 -------- -------------------------------------------------------- 428 -------- --------------------------------------------------------
411 1 QNAME seq-ID 429 1 QNAME seq-ID
412 2 FLAG this flag tries to take the strand a bisulfite read 430 2 FLAG this flag tries to take the strand a bisulfite read
413 originated from into account 431 originated from into account
414 (this is different from ordinary DNA alignment flags!) 432 (this is different from ordinary DNA alignment flags!)
415 3 RNAME chromosome 433 3 RNAME chromosome
416 4 POS start position 434 4 POS start position
417 5 MAPQ always 255 435 5 MAPQ always 255
418 6 CIGAR extended CIGAR string 436 6 CIGAR extended CIGAR string
420 8 MPOS 1-based Mate POSition 438 8 MPOS 1-based Mate POSition
421 9 ISIZE Inferred insert SIZE 439 9 ISIZE Inferred insert SIZE
422 10 SEQ query SEQuence on the same strand as the reference 440 10 SEQ query SEQuence on the same strand as the reference
423 11 QUAL Phred33 scale 441 11 QUAL Phred33 scale
424 12 NM-tag edit distance to the reference) 442 12 NM-tag edit distance to the reference)
425 13 XX-tag base-by-base mismatches to the reference. 443 13 XX-tag base-by-base mismatches to the reference.
426 This does not include indels. 444 This does not include indels.
427 14 XM-tag methylation call string 445 14 XM-tag methylation call string
428 15 XR-tag read conversion state for the alignment 446 15 XR-tag read conversion state for the alignment
429 16 XG-tag genome conversion state for the alignment 447 16 XG-tag genome conversion state for the alignment
430 448
431 449
432 Each read of paired-end alignments is written out in a separate line in the above format. 450 Each read of paired-end alignments is written out in a separate line in the above format.
433 451
434 452
435 It looks like this (scroll sideways to see the entire example):: 453 It looks like this (scroll sideways to see the entire example)::
482 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on. 500 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
483 501
484 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off. 502 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
485 503
486 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled 504 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
487 (which can't). The formula for conversion is: 505 (which can't). The formula for conversion is:
488 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This 506 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
489 is usually the right option for use with (unconverted) reads emitted by the GA 507 is usually the right option for use with (unconverted) reads emitted by the GA
490 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off. 508 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
491 509
492 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted) 510 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
494 512
495 513
496 Alignment:: 514 Alignment::
497 515
498 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs 516 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
499 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the 517 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
500 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N). 518 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
501 519
502 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to 520 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
503 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for 521 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
504 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L). 522 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
632 650
633 For reference, this used to be the old (now deprecated) description of -M: 651 For reference, this used to be the old (now deprecated) description of -M:
634 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it 652 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
635 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever 653 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
636 happens first. Only the best alignment is reported. Information from the other alignments is used to 654 happens first. Only the best alignment is reported. Information from the other alignments is used to
637 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes 655 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
638 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that 656 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
639 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not 657 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
640 guarantee that the alignment reported is the best possible in terms of alignment score. -M is 658 guarantee that the alignment reported is the best possible in terms of alignment score. -M is
641 always used and its default value is set to 10. 659 always used and its default value is set to 10.
642 660
661 ]]>
643 </help> 662 </help>
663 <citations>
664 <citation type="doi">10.1093/bioinformatics/btr167</citation>
665 </citations>
644 </tool> 666 </tool>