Mercurial > repos > bgruening > bismark

comparison bismark_bowtie_wrapper.xml @ 4:243e8f9fb75b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Mon, 09 Feb 2015 18:24:41 -0500
parents 91f07ff056ca
children b100248c35b8
comparison
equal deleted inserted replaced
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="0.12.8">bowtie</requirement> 8 <requirement type="package" version="0.12.8">bowtie</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 --bismark_path \$SCRIPT_PATH 20 ##--bismark_path \$SCRIPT_PATH
15 21
16 ## 22 ##
17 ## Bismark Genome Preparation, if desired. 23 ## Bismark Genome Preparation, if desired.
18 ## 24 ##
19 25
51 #end for 57 #end for
52 58
53 --mate1 #echo ','.join($mate1) 59 --mate1 #echo ','.join($mate1)
54 --mate2 #echo ','.join($mate2) 60 --mate2 #echo ','.join($mate2)
55 61
56 #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina": 62 #for $mate_pair in $singlePaired.mate_list:
57 --phred64-quals 63 #if $mate_pair.input_mate1.ext == "fastqillumina":
58 --fastq 64 --phred64-quals
59 #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger": 65 --fastq
60 --fastq 66 #elif $mate_pair.input_mate1.ext == "fastqsanger":
61 #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta": 67 --fastq
62 --fasta 68 #elif $mate_pair.input_mate1.ext == "fasta":
63 #end if 69 --fasta
70 #end if
71 #break
72 #end for
64 73
65 -I $singlePaired.minInsert 74 -I $singlePaired.minInsert
66 -X $singlePaired.maxInsert 75 -X $singlePaired.maxInsert
67 #end if 76 #end if
68 77
121 --output-suppressed-reads-l $output_suppressed_reads_l 130 --output-suppressed-reads-l $output_suppressed_reads_l
122 --output-suppressed-reads-r $output_suppressed_reads_r 131 --output-suppressed-reads-r $output_suppressed_reads_r
123 #end if 132 #end if
124 #end if 133 #end if
125 134
135 ]]>
126 </command> 136 </command>
127 <inputs> 137 <inputs>
128 <conditional name="refGenomeSource"> 138 <conditional name="refGenomeSource">
129 <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"> 139 <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">
130 <option value="indexed">Use a built-in index</option> 140 <option value="indexed">Use a built-in index</option>
189 <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." /> 199 <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." />
190 <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" /> 200 <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" />
191 <!-- output Options --> 201 <!-- output Options -->
192 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" /> 202 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
193 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" /> 203 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
194 <!--end output options --> 204 <!--end output options -->
195 </when> <!-- full --> 205 </when> <!-- full -->
196 </conditional> <!-- params --> 206 </conditional> <!-- params -->
197 <!-- 207 <!--
198 <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." /> 208 <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." />
199 --> 209 -->
249 <action type="format"> 259 <action type="format">
250 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 260 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
251 </action> 261 </action>
252 </when> 262 </when>
253 <when value="paired"> 263 <when value="paired">
254 <action type="format"> 264 <!--action type="format">
255 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 265 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
256 </action> 266 </action-->
257 </when> 267 </when>
258 </conditional> 268 </conditional>
259 </actions> 269 </actions>
260 </data> 270 </data>
261 271
269 <action type="format"> 279 <action type="format">
270 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 280 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
271 </action> 281 </action>
272 </when> 282 </when>
273 <when value="paired"> 283 <when value="paired">
274 <action type="format"> 284 <!--action type="format">
275 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 285 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
276 </action> 286 </action-->
277 </when> 287 </when>
278 </conditional> 288 </conditional>
279 </actions> 289 </actions>
280 </data> 290 </data>
281 291
293 <action type="format"> 303 <action type="format">
294 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 304 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
295 </action> 305 </action>
296 </when> 306 </when>
297 <when value="paired"> 307 <when value="paired">
298 <action type="format"> 308 <!--action type="format">
299 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 309 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
300 </action> 310 </action-->
301 </when> 311 </when>
302 </conditional> 312 </conditional>
303 </actions> 313 </actions>
304 </data> 314 </data>
305 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> 315 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
312 <action type="format"> 322 <action type="format">
313 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" /> 323 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
314 </action> 324 </action>
315 </when> 325 </when>
316 <when value="paired"> 326 <when value="paired">
317 <action type="format"> 327 <!--action type="format">
318 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" /> 328 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
319 </action> 329 </action-->
320 </when> 330 </when>
321 </conditional> 331 </conditional>
322 </actions> 332 </actions>
323 </data> 333 </data>
324
325
326 </outputs> 334 </outputs>
327 335
328 <tests> 336 <tests>
329 </tests> 337 </tests>
330 338
331 <help> 339 <help>
340 <![CDATA[
332 341
333 **What it does** 342 **What it does**
334 343
335 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the 344 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
336 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand 345 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
384 The output is in SAM format, and has the following columns:: 393 The output is in SAM format, and has the following columns::
385 394
386 Column Description 395 Column Description
387 -------- -------------------------------------------------------- 396 -------- --------------------------------------------------------
388 1 QNAME seq-ID 397 1 QNAME seq-ID
389 2 FLAG this flag tries to take the strand a bisulfite read 398 2 FLAG this flag tries to take the strand a bisulfite read
390 originated from into account 399 originated from into account
391 (this is different from ordinary DNA alignment flags!) 400 (this is different from ordinary DNA alignment flags!)
392 3 RNAME chromosome 401 3 RNAME chromosome
393 4 POS start position 402 4 POS start position
394 5 MAPQ always 255 403 5 MAPQ always 255
395 6 CIGAR extended CIGAR string 404 6 CIGAR extended CIGAR string
397 8 MPOS 1-based Mate POSition 406 8 MPOS 1-based Mate POSition
398 9 ISIZE Inferred insert SIZE 407 9 ISIZE Inferred insert SIZE
399 10 SEQ query SEQuence on the same strand as the reference 408 10 SEQ query SEQuence on the same strand as the reference
400 11 QUAL Phred33 scale 409 11 QUAL Phred33 scale
401 12 NM-tag edit distance to the reference) 410 12 NM-tag edit distance to the reference)
402 13 XX-tag base-by-base mismatches to the reference. 411 13 XX-tag base-by-base mismatches to the reference.
403 This does not include indels. 412 This does not include indels.
404 14 XM-tag methylation call string 413 14 XM-tag methylation call string
405 15 XR-tag read conversion state for the alignment 414 15 XR-tag read conversion state for the alignment
406 16 XG-tag genome conversion state for the alignment 415 16 XG-tag genome conversion state for the alignment
407 416
408 417
409 Each read of paired-end alignments is written out in a separate line in the above format. 418 Each read of paired-end alignments is written out in a separate line in the above format.
410 419
411 420
412 It looks like this (scroll sideways to see the entire example):: 421 It looks like this (scroll sideways to see the entire example)::
459 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on. 468 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
460 469
461 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off. 470 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
462 471
463 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled 472 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
464 (which can't). The formula for conversion is: 473 (which can't). The formula for conversion is:
465 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This 474 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
466 is usually the right option for use with (unconverted) reads emitted by the GA 475 is usually the right option for use with (unconverted) reads emitted by the GA
467 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off. 476 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
468 477
469 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted) 478 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
471 480
472 481
473 Alignment:: 482 Alignment::
474 483
475 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs 484 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
476 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the 485 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
477 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N). 486 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
478 487
479 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to 488 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
480 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for 489 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
481 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L). 490 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
544 553
545 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If 554 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
546 the specified folder does not exist, Bismark will attempt to create it first. The path to the 555 the specified folder does not exist, Bismark will attempt to create it first. The path to the
547 temporary folder can be either relative or absolute. 556 temporary folder can be either relative or absolute.
548 557
558 ]]>
549 </help> 559 </help>
560 <citations>
561 <citation type="doi">10.1093/bioinformatics/btr167</citation>
562 </citations>
550 </tool> 563 </tool>