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Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 24 Aug 2012 16:00:21 -0400
parents e54bb199a47b
children fcb60273c710
comparison
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4:e54bb199a47b 5:949ac66308a7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="freebayes" name="FreeBayes" version="0.0.2"> 2 <tool id="freebayes" name="FreeBayes" version="0.0.3">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.9.4_a46483351fd0196637614121868fb5c386612b55">freebayes</requirement> 4 <requirement type="package" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 <requirement type="package">samtools</requirement>
6 </requirements> 6 </requirements>
7 <description> - Bayesian genetic variant detector</description> 7 <description> - Bayesian genetic variant detector</description>
8 <command> 8 <command>
9 ##set up input files 9 ##set up input files
10 #set $reference_fasta_filename = "localref.fa" 10 #set $reference_fasta_filename = "localref.fa"
57 #end if 57 #end if
58 #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf": 58 #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf":
59 --variant-input "${options_type.input_variant_type.input_variant_vcf}" 59 --variant-input "${options_type.input_variant_type.input_variant_vcf}"
60 ${options_type.input_variant_type.only_use_input_alleles} 60 ${options_type.input_variant_type.only_use_input_alleles}
61 #end if 61 #end if
62 #if $options_type.haplotype_basis_alleles:
63 --haplotype-basis-alleles "${options_type.haplotype_basis_alleles}"
64 #end if
65
62 66
63 ##reporting 67 ##reporting
64 #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set": 68 #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":
65 --pvar "${options_type.section_reporting_type.pvar}" 69 --pvar "${options_type.section_reporting_type.pvar}"
66 ${options_type.section_reporting_type.show_reference_repeats} 70 ${options_type.section_reporting_type.show_reference_repeats}
96 ${options_type.left_align_indels} 100 ${options_type.left_align_indels}
97 101
98 ##input filters 102 ##input filters
99 #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set": 103 #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set":
100 ${options_type.section_input_filters_type.use_duplicate_reads} 104 ${options_type.section_input_filters_type.use_duplicate_reads}
101 #if str( $options_type.section_input_filters_type.no_filter_type.no_filter_type_selector ) == "apply_filters": 105 #if str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "apply_filters":
102 --min-mapping-quality "${options_type.section_input_filters_type.no_filter_type.min_mapping_quality}" 106 --min-mapping-quality "${options_type.section_input_filters_type.quality_filter_type.min_mapping_quality}"
103 --min-base-quality "${options_type.section_input_filters_type.no_filter_type.min_base_quality}" 107 --min-base-quality "${options_type.section_input_filters_type.quality_filter_type.min_base_quality}"
104 --min-supporting-quality "${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_bq}" 108 --min-supporting-quality "${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_bq}"
105 #else: 109 #elif str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "standard_filters":
106 --no-filters 110 --standard-filters
107 #end if 111 #end if
108 --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}" 112 --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}"
109 #if $options_type.section_input_filters_type.read_mismatch_limit: 113 #if $options_type.section_input_filters_type.read_mismatch_limit:
110 --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}" 114 --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}"
111 #end if 115 #end if
231 <when value="provide_vcf"> 235 <when value="provide_vcf">
232 <param name="input_variant_vcf" type="data" format="vcf" label="Use variants reported in VCF file as input to the algorithm" /> 236 <param name="input_variant_vcf" type="data" format="vcf" label="Use variants reported in VCF file as input to the algorithm" />
233 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" /> 237 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />
234 </when> 238 </when>
235 </conditional> 239 </conditional>
236 240 <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" />
237 241
238 <!-- reporting --> 242 <!-- reporting -->
239 <conditional name="section_reporting_type"> 243 <conditional name="section_reporting_type">
240 <param name="section_reporting_type_selector" type="select" label="Set Reporting options"> 244 <param name="section_reporting_type_selector" type="select" label="Set Reporting options">
241 <option value="do_not_set" selected="True">Do not set</option> 245 <option value="do_not_set" selected="True">Do not set</option>
314 <when value="do_not_set"> 318 <when value="do_not_set">
315 <!-- do nothing here --> 319 <!-- do nothing here -->
316 </when> 320 </when>
317 <when value="set"> 321 <when value="set">
318 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" /> 322 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" />
319 <conditional name="no_filter_type"> 323 <conditional name="quality_filter_type">
320 <param name="no_filter_type_selector" type="select" label="Apply filters"> 324 <param name="quality_filter_type_selector" type="select" label="Apply Quality filters">
321 <option value="apply_filters" selected="True">Apply</option> 325 <option value="standard_filters" selected="True">Apply standard</option>
322 <option value="no_filters">Do not apply</option> 326 <option value="apply_filters">Apply specified</option>
323 </param> 327 </param>
324 <when value="no_filters"> 328 <when value="standard_filters">
325 <!-- Do nothing here --> <!-- no-filters --> 329 <!-- Do nothing here --> <!-- standard-filters -->
326 </when> 330 </when>
327 <when value="apply_filters"> 331 <when value="apply_filters">
328 <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="30" /> 332 <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="0" />
329 <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="20" /> 333 <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="0" />
330 <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" /> 334 <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" />
331 <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" /> 335 <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" />
332 </when> 336 </when>
333 </conditional> 337 </conditional>
334 <param name="mismatch_base_quality_threshold" type="integer" label="Count mismatches toward read-mismatch-limit if the base quality of the mismatch is &gt;=" value="10" /> 338 <param name="mismatch_base_quality_threshold" type="integer" label="Count mismatches toward read-mismatch-limit if the base quality of the mismatch is &gt;=" value="10" />
421 <param name="reference_source_selector" value="history" /> 425 <param name="reference_source_selector" value="history" />
422 <param name="ref_file" ftype="fasta" value="phiX.fasta"/> 426 <param name="ref_file" ftype="fasta" value="phiX.fasta"/>
423 <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/> 427 <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/>
424 <param name="options_type_selector" value="basic"/> 428 <param name="options_type_selector" value="basic"/>
425 <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/> 429 <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/>
426 <!-- <output name="output_failed_alleles_bed" file="empty_file.dat" />
427 <output name="output_trace" file="freebayes_out_1.output_trace" /> -->
428 </test> 430 </test>
429 </tests> 431 </tests>
430 <help> 432 <help>
431 **What it does** 433 **What it does**
432 434
492 -l --only-use-input-alleles 494 -l --only-use-input-alleles
493 Only provide variant calls and genotype likelihoods for sites 495 Only provide variant calls and genotype likelihoods for sites
494 and alleles which are provided in the VCF input, and provide 496 and alleles which are provided in the VCF input, and provide
495 output in the VCF for all input alleles, not just those which 497 output in the VCF for all input alleles, not just those which
496 have support in the data. 498 have support in the data.
499 --haplotype-basis-alleles VCF
500 When specified, only variant alleles provided in this input
501 VCF will be used for the construction of complex or haplotype
502 alleles.
497 503
498 reporting: 504 reporting:
499 505
500 -P --pvar N Report sites if the probability that there is a polymorphism 506 -P --pvar N Report sites if the probability that there is a polymorphism
501 at the site is greater than N. default: 0.0001 507 at the site is greater than N. default: 0.0001
575 with quality &gt;= mismatch-base-quality-threshold. 581 with quality &gt;= mismatch-base-quality-threshold.
576 default: ~unbounded 582 default: ~unbounded
577 -e --read-indel-limit N 583 -e --read-indel-limit N
578 Exclude reads with more than N separate gaps. 584 Exclude reads with more than N separate gaps.
579 default: ~unbounded 585 default: ~unbounded
580 -0 --no-filters Do not use any input base and mapping quality filters 586 -0 --standard-filters Use stringent input base and mapping quality filters
581 Equivalent to -m 0 -q 0 -R 0 -S 0 587 Equivalent to -m 30 -q 20 -R 0 -S 0
582 -x --indel-exclusion-window 588 -x --indel-exclusion-window
583 Ignore portions of alignments this many bases from a 589 Ignore portions of alignments this many bases from a
584 putative insertion or deletion allele. default: 0 590 putative insertion or deletion allele. default: 0
585 -F --min-alternate-fraction N 591 -F --min-alternate-fraction N
586 Require at least this fraction of observations supporting 592 Require at least this fraction of observations supporting
660 666
661 ------ 667 ------
662 668
663 **Citation** 669 **Citation**
664 670
665 For the underlying tool, please cite `FreeBayes &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_. 671 For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing &lt;http://arxiv.org/abs/1207.3907&gt;`_.
666 672
667 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* 673 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
668 674
669 </help> 675 </help>
670 </tool> 676 </tool>